Microbial engineering for the production of chemical and pharmaceutical products from the isoprenoid pathway

ABSTRACT

The invention relates to recombinant expression of a taxadiene synthase enzyme and a geranylgeranyl diphosphate synthase (GGPPS) enzyme in cells and the production of terpenoids.

RELATED APPLICATIONS

This application claims the benefit under 35 U.S.C. §119(e) of U.S.Provisional Application Ser. No. 61/280,877, entitled “MicrobialEngineering for the Production of Chemical and Pharmaceutical Productsfrom Isoprenoid Pathway,” filed on Nov. 10, 2009 and U.S. ProvisionalApplication Ser. No. 61/388,543, entitled “Microbial Engineering for theProduction of Chemical and Pharmaceutical Products from IsoprenoidPathway,” filed on Sep. 30, 2010, the entire disclosures of which areincorporated by reference herein in their entireties.

GOVERNMENT INTEREST

This invention was made with government support under Grant No. GM085323awarded by the National Institutes of Health. The government has certainrights in this invention.

FIELD OF THE INVENTION

The invention relates to the production of one or more terpenoidsthrough microbial engineering.

BACKGROUND OF THE INVENTION

Taxol and its structural analogs have been recognized as the most potentand commercially successful anticancer drugs introduced in the lastdecade.¹ Taxol was first isolated from the bark of the Pacific Yewtree,² and early stage production methods required sacrificing two tofour fully grown trees to supply sufficient dosage for one patient.³Taxol's structural complexity necessitated a complex chemical synthesisroute requiring 35-51 steps with highest yield of 0.4%.^(4,5,6) However,a semi-synthetic route was devised whereby the biosynthetic intermediatebaccatin III was first isolated from plant sources and was subsequentlyconverted to Taxol.⁷ While this approach and subsequent plant cellculture-based production efforts have decreased the need for harvestingthe yew tree, production still depends on plant-based processes⁸ withaccompanying limitations of productivity and scalability, andconstraints on the number of Taxol derivatives that can be synthesizedin search for more efficacious drugs.^(9,10)

SUMMARY OF THE INVENTION

Recent developments in metabolic engineering and synthetic biology offernew possibilities for the overproduction of complex natural productsthrough more technically amenable microbial hosts.^(11,12) Althoughexciting progress has been made in the elucidation of the biosyntheticmechanism of Taxol in Taxus, ¹³⁻¹⁶ commercially relevant Taxol-producingstrains have eluded prior attempts aiming at the transfer of thiscomplex biosynthetic machinery into a microbial host.^(17,18) Yet, aswith other natural products, microbial production through metabolicallyengineered strains, offers attractive economics and great potential forsynthesizing a diverse array of new compounds with anti-cancer and otherpharmaceutical activity.^(19,20)

The metabolic pathway for Taxol and its analogs consists of an upstreamisoprenoid pathway that is native to E. coli, and a heterologousdownstream terpenoid pathway (FIG. 6).

The upstream mevalonic acid (MVA) or methylerythritol phosphate (MEP)pathways can produce the two common building blocks, isopentenylpyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), from whichTaxol and other isoprenoid compounds are formed.¹² Recent studies havehighlighted the engineering of the above upstream pathways to supportbiosynthesis of heterologous isoprenoids such as lycopene andartemisinic acid.²¹⁻²³ The downstream taxadiene pathway has beenreconstructed in E. coli, but, to-date, titers have not exceeded 1.3mg/L.²⁴

The above rational metabolic engineering approaches focused on eitherthe upstream (MVA or MEP) or the downstream terpenoid pathway,implicitly assuming that modifications are additive, i.e. a linearbehavior.²⁵⁻²⁷ While this approach can yield moderate increases in flux,it generally ignores non-specific effects, such as toxicity ofintermediate metabolites, cellular effects of the vectors used forexpression, and hidden unknown pathways that may compete with the mainpathway and divert flux away from the desired target. Combinatorialapproaches can avoid such problems as they offer the opportunity toadequately sample the parameter space and elucidate these complexnon-linear interactions.^(21,28,29,30) However, they require a highthroughput screen, which is often not available for many desirablenatural products.³¹ Yet another class of pathway optimization methodshas explored the combinatorial space of different sources of theheterologous genes comprising the pathway of interest.³² Still dependenton a high throughput assay, these methods generally ignore the need fordetermining an optimal level of expression for the individual pathwaygenes and, as such, have proven less effective in structuring an optimalpathway.

In the present work, as an example of aspects of the invention, we focuson the optimal balancing between the upstream, IPP-forming pathway withthe downstream terpenoid pathway of taxadiene synthesis. This isachieved by grouping the nine-enzyme pathway into two modules—afour-gene, upstream, native (MEP) pathway module and a two-gene,downstream, heterologous pathway to taxadiene (FIG. 1). Using this basicconfiguration, parameters such as the effect of plasmid copy number oncell physiology, gene order and promoter strength in an expressioncassette, and chromosomal integration are evaluated with respect totheir effect on taxadiene production. This modular and multivariablecombinatorial approach allows us to efficiently sample the mainparameters affecting pathway flux without the need for a high throughputscreen. The multivariate search across multiple promoters and copynumbers for each pathway module reveals a highly non-linear taxadieneflux landscape with a global maximum exhibiting a 15,000 fold increasein taxadiene production over the control, yielding 300 mg/L productionof taxadiene in small-scale fermentations. Further, we have engineeredthe P450 based oxidation chemistry in Taxol biosynthesis in E. coli,with our engineered strains improving the taxadien-5α-ol production2400-fold over the state of the art. These improvements unlock thepotential for the large scale production of thousands of valuableterpenoids by well-established microbial systems.

Aspects of the invention relate to methods involving recombinantlyexpressing a taxadiene synthase enzyme and a geranylgeranyl diphosphatesynthase (GGPPS) enzyme in a cell that overexpresses one or morecomponents of the non-mevalonate (MEP) pathway. In some embodiments thecell is a bacterial cell such as an Escherichia coli cell. In someembodiments, the bacterial cell is a Gram-positive cell such as aBacillus cell. In some embodiments, the cell is a yeast cell such as aSaccharomyces cell or a Yarrowia cell. In some embodiments, the cell isan algal cell or a plant cell.

In some embodiments, the taxadiene synthase enzyme is a Taxus enzymesuch as a Taxus brevifolia enzyme. In some embodiments, the GGPPS enzymeis a Taxus enzyme such as a Taxus canadenis enzyme. In some embodiments,the gene encoding for the taxadiene synthase enzyme and/or the geneencoding for the GGPPS enzyme and/or the genes encoding for the one ormore components of the MEP pathway is expressed from one or moreplasmids. In some embodiments, the gene encoding for the taxadienesynthase enzyme and/or the gene encoding for the GGPPS enzyme and/or thegenes encoding for the one or more components of the MEP is incorporatedinto the genome of the cell.

In some embodiments, one or more components of the non-mevalonate (MEP)pathway are selected from the group consisting of dxs, ispC, ispD, ispE,ispF, ispG, ispH, idi, ispA and ispB. In certain embodiments, dxs, idi,ispD and ispF are overexpressed. For example, dxs, idi, ispD and ispFcan be overexpressed on the operon dxs-idi-idpDF. In some embodiments,the gene encoding for the taxadiene synthase enzyme and the geneencoding for the GGPPS enzyme are expressed together on an operon.

In some embodiments, the cell further expresses a taxadiene5α-hydroxylase (T5αOH) or a catalytically active portion thereof. Incertain embodiments, the T5αOH enzyme or a catalytically active portionthereof is fused to a cytochrome P450 reductase enzyme or acatalytically active portion thereof. For example, the T5αOH enzyme canbe At24T5αOH-tTCPR.

The expression of the taxadiene synthase enzyme, the GGPPS enzyme andthe one or more components of the MEP pathway can be balanced tomaximize production of the taxadiene. Methods associated with theinvention can further encompass culturing a cell to produce taxadiene ortaxadiene-5α-ol. In some embodiments, at least 10 mg L⁻¹ of taxadiene isproduced. In certain embodiments, at least 250 mg L⁻¹ of taxadiene isproduced. In some embodiments, at least 10 mg L⁻¹ of taxadiene-5α-ol isproduced. In certain embodiments, at least 50 mg L⁻¹ of taxadiene-5α-olis produced. In some embodiments, the percentage of taxadiene conversionto taxadiene-5α-ol and the byproduct 5(12)-Oxa-3(11)-cyclotaxane is atleast 50%, at least 75% or at least 95%.

Methods associated with the invention can further comprise recoveringthe taxadiene or taxadiene-5α-ol from the cell culture. In someembodiments, the taxadiene or taxadiene-5α-ol is recovered from the gasphase while in other embodiments, an organic layer is added to the cellculture, and the taxadiene or taxadiene-5α-ol is recovered from theorganic layer.

Aspects of the invention relate to cells that overexpress one or morecomponents of the non-mevalonate (MEP) pathway, and that recombinantlyexpresses a taxadiene synthase enzyme and a geranylgeranyl diphosphatesynthase (GGPPS) enzyme. In some embodiments the cell is a bacterialcell such as an Escherichia coli cell. In some embodiments, thebacterial cell is a Gram-positive cell such as a Bacillus cell. In someembodiments, the cell is a yeast cell such as a Saccharomyces cell or aYarrowia cell. In some embodiments, the cell is an algal cell or a plantcell.

In some embodiments, the taxadiene synthase enzyme is a Taxus enzymesuch as a Taxus brevifolia enzyme. In some embodiments, the GGPPS enzymeis a Taxus enzyme such as a Taxus canadenis enzyme. In some embodiments,the gene encoding for the taxadiene synthase enzyme and/or the geneencoding for the GGPPS enzyme and/or the genes encoding for the one ormore components of the MEP pathway is expressed from one or moreplasmids. In some embodiments, the gene encoding for the taxadienesynthase enzyme and/or the gene encoding for the GGPPS enzyme and/or thegenes encoding for the one or more components of the MEP is incorporatedinto the genome of the cell.

In some embodiments, the one or more components of the non-mevalonate(MEP) pathway is selected from the group consisting of dxs, ispC, ispD,ispE, ispF, ispG, ispH, idi, ispA and ispB. In certain embodiments, dxs,idi, ispD and ispF are overexpressed. For example, dxs, idi, ispD andispF can be overexpressed on the operon dxs-idi-idpDF. In someembodiments, the gene encoding for the taxadiene synthase enzyme and thegene encoding for the GGPPS enzyme are expressed together on an operon.In some embodiments, the expression of the taxadiene synthase enzyme,the GGPPS enzyme and the one or more components of the MEP pathway arebalanced to maximize production of the taxadiene.

In some embodiments, the cell further expresses a taxadiene5α-hydroxylase (T5αOH) or a catalytically active portion thereof. Incertain embodiments, the T5αOH enzyme or a catalytically active portionthereof is fused to a cytochrome P450 reductase enzyme or acatalytically active portion thereof. For example, the T5αOH enzyme canbe At24T5αOH-tTCPR. In some embodiments, the cell produces taxadieneand/or taxadiene-5α-ol.

Aspects of the invention relate to methods for selecting a cell thatexhibits enhanced production of a terpenoid, including creating orobtaining a cell that overexpresses one or more components of thenon-mevalonate (MEP) pathway, producing terpenoid from the cell,comparing the amount of terpenoid produced from the cell to the amountof terpenoid produced in a control cell, and selecting a first improvedcell that produces a higher amount of terpenoid than a control cell,wherein a first improved cell that produces a higher amount of terpenoidthan the control cell is a cell that exhibits enhanced production ofterpenoid.

In some embodiments, the cell recombinantly expresses a terpenoidsynthase enzyme and/or a geranylgeranyl diphosphate synthase (GGPPS)enzyme. Methods can further comprise altering the level of expression ofone or more of the components of the non-mevalonate (MEP) pathway, theterpenoid synthase enzyme and/or the geranylgeranyl diphosphate synthase(GGPPS) enzyme in the first improved cell to produce a second improvedcell, and comparing the amount of terpenoid produced from the secondimproved cell to the amount of terpenoid produced in the first improvedcell, wherein a second improved cell that produces a higher amount ofterpenoid than the first improved cell is a cell that exhibits enhancedproduction of terpenoid. In some embodiments, the terpenoid synthaseenzyme is a taxadiene synthase enzyme. The cell can furtherrecombinantly express any of the polypeptides associated with theinvention.

Aspects of the invention relate to isolated polypeptides comprising ataxadiene 5α-hydroxylase (T5αOH) enzyme or a catalytically activeportion thereof fused to a cytochrome P450 reductase enzyme or acatalytically active portion thereof. In some embodiments, thecytochrome P450 reductase enzyme is a Taxus cytochrome P450 reductase(TCPR). In certain embodiments, the taxadiene 5α-hydroxylase and TCPRare joined by a linker such as GSTGS (SEQ ID NO:50). In someembodiments, the taxadiene 5α-hydroxylase and/or TCPR are truncated toremove all or part of the transmembrane region. In certain embodiments,8, 24, or 42 N-terminal amino acids of taxadiene 5α-hydroxylase aretruncated. In certain embodiments, 74 amino acids of TCPR are truncated.In some embodiments, an additional peptide is fused to taxadiene5α-hydroxylase. In certain embodiments, the additional peptide is frombovine 17α hydroxylase. In certain embodiments, the peptide is MALLLAVF(SEQ ID NO:51). In certain embodiments, the isolated polypeptide isAt24T5αOH-tTCPR. Aspects of the invention also encompass nucleic acidmolecules that encode for any of the polypeptides associated with theinvention and cells that recombinantly express any of the polypeptidesassociated with the invention.

Aspects of the invention relate to methods for increasing terpenoidproduction in a cell that produces one or more terpenoids. The methodsinclude controlling the accumulation of indole in the cell or in aculture of the cells, thereby increasing terpenoid production in a cell.Any of the cells described herein can be used in the methods, includingbacterial cells, such as Escherichia coli cells; Gram-positive cells,such as Bacillus cells; yeast cells, such as Saccharomyces cells orYarrowia cells; algal cells; plant cell; and any of the engineered cellsdescribed herein.

In some embodiments, the step of controlling the accumulation of indolein the cell or in a culture of the cells includes balancing the upstreamnon-mevalonate isoprenoid pathway with the downstream product synthesispathways and/or modifying or regulating the indole pathway. In otherembodiments, the step of controlling the accumulation of indole in thecell or in a culture of the cells includes or further includes removingthe accumulated indole from the fermentation through chemical methods,such as by using absorbents or scavengers.

The one or more terpenoids produced by the cell(s) or in the culture canbe a monoterpenoid, a sesquiterpenoid, a diterpenoid, a diterpenoid or atetraterpenoid. In certain embodiments, the terpenoids is taxadiene orany taxol precursor.

Aspects of the invention relate to methods that include measuring theamount or concentration of indole in a cell that produces one or moreterpenoids or in a culture of the cells that produce one or moreterpenoids. The methods can include measuring the amount orconcentration of indole two or more times. In some embodiments, themeasured amount or concentration of indole is used to guide a process ofproducing one or more terpenoids. In some embodiments, the measuredamount or concentration of indole is used to guide strain construction.

These and other aspects of the invention, as well as various embodimentsthereof, will become more apparent in reference to the drawings anddetailed description of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings are not intended to be drawn to scale. In thedrawings, each identical or nearly identical component that isillustrated in various figures is represented by a like numeral. Forpurposes of clarity, not every component may be labeled in everydrawing. In the drawings:

FIG. 1. Multivariate-modular isoprenoid pathway engineering revealsstrong non-linear response in terpenoid accumulation. To increase theflux through the upstream MEP pathway, we targeted reported bottleneckenzymatic steps (dxs, idi, ispD and ispF) for overexpression by anoperon (dxs-idi-ispDF).²⁸ To channel the overflow flux from theuniversal isoprenoid precursors, IPP and DMAPP, towards Taxolbiosynthesis, a synthetic operon of downstream genes GGPP synthase (G)and Taxadiene synthase (T)¹⁶ was constructed. The upstream isoprenoidand downstream synthetic taxadiene pathways were placed under thecontrol of inducible promoters to control their relative geneexpression. (a) Schematic of the two modules, the native upstream MEPisoprenoid pathway (left) and synthetic taxadiene pathway (right). In E.coli biosynthetic network, the MEP isoprenoid pathway is initiated bythe condensation of the precursors glyceraldehydes-3 phosphate (G3P) andpyruvate (PYR) from glycolysis. The Taxol pathway bifurcation startsfrom the universal isoprenoid precursors IPP and DMAPP to form first the“linear” precursor Geranylgeranyl diphosphate, and then the “cyclic”taxadiene, a committed and key intermediate to Taxol. The cyclic olefintaxadiene undergoes multiple rounds of stereospecific oxidations,acylations, benzoylation with side chain assembly to, ultimately, formTaxol. (b) Schematic of the multivariate-modular isoprenoid pathwayengineering approach for probing the non-linear response in terpenoidaccumulation from upstream and downstream pathway engineered cells.Expression of upstream and downstream pathways is modulated by varyingthe promoter strength (Trc, T5 and T7) or increasing the copy numberusing different plasmids. Variation of upstream and downstream pathwayexpression gives different maxima in taxadiene accumulation.

FIG. 2. Optimization of taxadiene production by regulating theexpression of the up- and down-stream modular pathways. (a) Response intaxadiene accumulation to the increase in upstream pathway strengths forconstant values of the downstream pathway. (b) the dependence on thedownstream pathway for constant increases in the upstream pathwaystrength. Observed multiple local maxima in taxadiene response dependson the increase in the pathway expression strength upstream ordownstream. (c) Taxadiene response from strains engineered (17-24) withhigh upstream pathway overexpressions (20-100) with two differentdownstream expressions (˜30 and ˜60) to identify taxadiene response withbalanced expressions. Expression of downstream pathway from the low copyplasmid (p5 and p10) under strong promoter T7TG operon was used tomodulate these expressions. Note that both upstream and downstreampathway expressed from different plasmids with different promoters canimpose plasmid born metabolic burden. (d) Modulating the upstreampathway with increasing promoter strength from chromosome with twodifferent downstream expressions (˜30 and ˜60) to identify the missingsearch space with reduced toxic effects (strains 25-32). (e) Geneticdetails of the taxadiene producing strains. The numbers corresponding todifferent strains and its corresponding genotype, E-E. coli K12mG1655ΔrecAΔendA, EDE3-E. coli K12mG1655 ΔrecAΔendA with T7 RNA polymerase DE3construct in the chromosome, MEP—dxs-idi-ispDF operon, GT—GPPS-TSoperon, TG—TS-GPPS operon, Ch1—1 copy in chromosome, Trc—Trc promoter,T5—T5 promoter, T7—T7 promoter, p5, p10, p20—˜5 (SC101), ˜10 (p15), and˜20 (pBR322) copy plasmid.

FIG. 3. Metabolite inversely correlates with taxadiene production. (a)Mass spectrum of metabolite that was detected to correlate inverselywith taxadiene production in the strain constructs of FIG. 2. Theobserved characteristic peaks of the metabolite are 233, 207, 178, 117,89 and 62. (b) Correlation between the isoprenoid byproduct of FIG. 3 aand taxadiene. Strains 26-29 and 30-32, all with chromosomallyintegrated upstream pathway expression, were chosen for consistentcomparison. In strains 26-29 and 30-32, upstream expression increased bychanging the promoters from Trc, to T5 and T7 respectively. The two setsof strains differ only in the expression of the downstream pathway withthe second set (30-32) having twice the level of expression of thefirst. With the first set, optimal balancing is achieved with strain 26,which uses the Trc promoter for upstream pathway expression and alsoshows the lowest metabolite accumulation. With strains 30-32, strain 31shows the lowest accumulation of metabolite and highest production oftaxadiene. The data demonstrate the inverse correlation observed betweenthe unknown metabolite and taxadiene production.

FIG. 4. Upstream and downstream pathway transcriptional gene expressionlevels and changes in cell physiology of engineered strains. Relativeexpression of the first genes in the operon of upstream (DXS) anddownstream (TS) pathway is quantified by qPCR. Similar expressionprofiles were observed with the genes in the downstream of the operons.The corresponding strain numbers are shown in the graph. (a) Relativetranscript level DXS gene expression quantified from different upstreamexpressions modulated using promoters and plasmids under two differentdownstream expressions. (b) Relative transcript level TS gene expressionquantified from two different downstream expression modulated using p5T7and p10T7 plasmids under different upstream expressions. Our geneexpression analysis directly supported the hypothesis, with increase inplasmid copy number (5, 10 and 20) and promoter strength (Trc, T5 andT7) the expression of the upstream and downstream pathways can bemodulated. (c) Cell growth of the engineered strains 25-29. The growthphenotype was affected from activation of isoprenoid metabolism (strain26), recombinant protein expression (strain 25) and plasmid bornmetabolic burden (control vs engineered strains) and (d) growthphenotypes of strains 17, 22, 25-32. The black color lines are thetaxadiene producing engineered strains and the gray color lines arecontrol strains without downstream expression carrying an empty plasmidwith promoter and multi cloning sites. The growth was correlated to theactivation of the terpenoid metabolism, plasmid born metabolic burden aswell the recombinant protein expression.

FIG. 5. Engineering Taxol p450 oxidation chemistry in E. coli. (a)Schematics of the conversion of taxadiene to taxadiene 5α-ol to Taxol.(b) Transmembrane engineering and construction of one-component chimeraprotein from taxadiene 5α-ol hydroxylsase (T5αOH) and Taxus cytochromep450 reductase (TCPR). 1 and 2 represents the full length proteins ofT5αOH and TCPR identified with 42 and 74 amino acid TM regionsrespectively, 3—chimera enzymes generated from the three different TMengineered T5αOH constructs, (At8T5αOH, At24T5αOH and At42T5αOHconstructed by fusing 8 residue synthetic peptide (A) to 8, 24 and 42 AAtruncated T5αOH) through a translational fusion with 74 AA truncatedTCPR (tTCPR) using 5 residue GSTGS linker peptide. (c) Functionalactivity of At8T5αOH-tTCPR, At24T5αOH-tTCPR and At42T5αOH-tTCPRconstructs transformed into taxadiene producing strain 18. (d) Timecourse profile of taxadien-5α-ol accumulation and growth profile of thestrain 18-At24T5αOH-tTCPR fermented in a 1 L bioreactor.

FIG. 6. Biosynthetic scheme for taxol production in E. coli. Schematicsof the two modules, native upstream isoprenoid pathway (left) andsynthetic Taxol pathway (right). In E. coli biosynthetic network,divergence of MEP isoprenoid pathway initiates from the precursorsglyceraldehyde-3 phosphate (G3P) and Pyruvate (PYR) from glycolysis(I-V). The Taxol pathway bifurcation starts from the E. coli isoprenoidprecursor IPP and DMAPP to “linear” precursor Geranylgeranyl diphosphate(VIII), “cyclic” taxadiene (IX), “oxidized” taxadiene 5α-ol (X) tomultiple rounds of stereospecific oxidations, acylations, benzoylationsand epoxidation for early precursor Baccatin III (XII) and finally withside chain assembly to Taxol (XIII). DXP—1-deoxy-D-xylulose-5-phosphate,MEP—2C-methyl-D-erythritol-4-phosphate,CDP-ME—4-diphosphocytidyl-2Cmethyl-D-erythritol,CDP-MEP—4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate,ME-cPP—2C-methyl-D-erythritol-2,4-cyclodiphosphate, IPP—isopentenyldiphosphate, DMAPP—dimethylallyl diphosphate. The genes involvedbiosynthetic pathways from G3P and PYR to Taxol.DXS-1-deoxy-D-xylulose-5-phosphate synthase,ispC-1-Deoxy-D-xylulose-5-phosphate reductoisomerase,IspD-4-diphosphocytidyl-2C-methyl-D-erythritol synthase,IspE-4-diphosphocytidyl-2-C-methyl-D-erythritol kinase,IspF-2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase,IspG-1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate synthase,IspH-4-hydroxy-3-methyl-2-(E)-butenyl-4-diphosphate reductaseIDI-isopentenyl-diphosphate isomerase, GGPPS—geranyl geranyldiphosphatesynthase, Taxadiene synthase, Taxoid 5α-hydroxylase,Taxoid-5α-O-acetyltransferase, Taxoid 13α-hydroxylase, Taxoid10β-hydroxylase, Taxoid 2α-hydroxylase, Taxoid 2-O-benzoyltransferase,Taxoid 7β-hydroxylase, Taxoid 10-O-acetyltransferase, Taxoid1β-hydroxylase*, Taxoid 9α-hydroxylase, Taxoid 9-keto-oxidase*, TaxoidC4,C20-β-epoxidase*, Phenylalanine aminomutase, Side chain CoA-ligase*,Taxoid 13 O-phenylpropanoyltransferase, Taxoid 2′-hydroxylase*, Taxoid3′-N-benzoyltransferase.^(216,219) * marked genes are yet to beidentified or characterized.

FIG. 7. Fold improvements in taxadiene production from the modularpathway expression search. (a) Taxadiene response in fold improvementsfrom all the observed maximas from FIG. 2 a,b, and c compared tostrain 1. The 2.5 fold differences between two highest maximas (strain17 and 26) and 23 fold (strain 26 and 10) with lowest one indicates thatmissing an optimal response results in significantly lower titers.

FIG. 8. Metabolite (a) Correlation between taxadiene to metaboliteaccumulation. The metabolite accumulation from the engineered strain isanti-proportionally related to the taxadiene production in anexponential manner. The correlation coefficient for this relation wasdetermined to 0.92 (b) Representative GC-profile from the strains 26-28to demonstrate the change in taxadiene and metabolite accumulation.Numbers in the chromatogram 1 and 2 corresponding to metabolite andtaxadiene peak respectively. (c) GC-MS profile of metabolite (1) andtaxadiene (2) respectively. The observed characteristic peaks of themetabolite are 233, 207, 178, 117, 89 and 62. Taxa-4(20),11,12-dienecharacteristic ion m/z 272(P⁺), 257 (P⁺—CH3), 229 (P⁺—C₃H₇); 121, 122,123 (C-ring fragment cluster).⁶⁰ The peak marked with a star is theinternal standard caryophylene.

FIG. 9. GC-MS profiles and taxadiene/taxadien-5α-ol production fromartificial chimera enzyme engineered in strain 26. (a) GC profile of thehexane:ether (8:2) extract from three constructs (A-At8T5αOH-tTCPR,t24T5αOH-tTCPR and At42T5αOH-tTCPR) transferred to strain 26 andfermented for 5 days. 1, 2 and 3 labels in the peaks corresponding tothe taxadiene, taxadien-5α-ol and 5(12)-Oxa-3(11)-cyclotaxane (OCT)respectively. (b) The production of taxa-4(20),11,12-dien-5α-ol and OCTquantified from the three strains. (c) and (d) GC-MS profile oftaxa-4(20),11,12-dien-5α-ol and OCT and the peaks corresponding to thefragmentation was compared with the authentic standards and previousreports^(42,47) GC-MS analysis confirmed the mass spectrum identity toauthentic taxa-4(20),11,12-dien-5α-ol with characteristic ion mh288(P⁺), 273 (P⁺—H₂O), 255 (P⁺—H₂O—CH3).

FIG. 10 presents a schematic depicting the terpenoid biosyntheticpathway and natural products produced by this pathway.

FIG. 11 presents a schematic depicting modulation of the upstreampathway for amplifying taxadiene production.

FIG. 12 presents a schematic depicting modulation of the downstreampathway for amplifying taxadiene production.

FIG. 13 presents a schematic indicating that the newly identifiedpathway diversion is not the characteristic of downstream syntheticpathway.

FIG. 14. Pathway strength correlates to transcriptional gene expressionlevels. (c) relative expression of idi, ispD and ispF genes withincreasing upstream pathway strength and downstream strength at 31arbitrary units, and (d) relative expression of idi, ispD and ispF geneswith increasing upstream pathway strength and downstream strength at 61arbitrary units. As expected the gene expression increased as theupstream pathway strength increased. The corresponding strain numbersare indicated in the bar graph. The relative expression was quantifiedusing the expression of the housekeeping rrsA gene. Data are mean+/−SDfor four replicates.

FIG. 15. Impact of metabolite byproduct Indole accumulation on taxadieneproduction and growth. (a) Inverse correlation between taxadiene andIndole. Strains 26 to 28 and 30 to 32, all with chromosomally integratedupstream pathway expression, were chosen for consistent comparison. Thetwo sets of strains differ only in the expression of the downstreampathway with the second set (30 to 32) having twice the level ofexpression of the first. In strains 26 to 28 and 30 to 32, upstreamexpression increased by changing the promoters from Trc, to T5 and T7,respectively. With the first set, optimal balancing is achieved withstrain 26, which uses the Trc promoter for upstream pathway expressionand also shows the lowest indole accumulation. With strains 30 to 32,strain 31 shows the lowest accumulation of indole and highest productionof taxadiene. The fold improvements are relative to strain 25 and 29,respectively, for the two sets. (b) Effect of externally-introducedindole on taxadiene production for the high-producing strain 26.Different concentrations of indole were introduced into cultures ofcells cultured in minimal media with 0.5% yeast extract. Taxadieneproduction was significantly reduced as indole concentration increasedfrom 50 mg/L to 100 mg/L (c) Effect of externally-introduced indole oncell growth for engineered strains of E. coli. Data are mean+/−SD forthree replicates. Strains devoid of the downstream pathway and withdifferent strengths of the upstream pathway (1, 2, 6, 21, 40 and 100)were selected. Strain 26, the high taxadiene producer, exhibits thestrongest inhibition.

FIG. 16. Unknown metabolite identified as indole. (A) and (a) Gaschromatogram and mass spectrum of the unknown metabolite extracted usinghexane from cell culture. (B) and (b) correspond to the gas chromatogramand mass spectrum of pure indole dissolved in hexane. Further to confirmthe chemical identity, the metabolite was extracted from thefermentation broth using hexane extraction and purified by silica columnchromatography using hexane:ethylacetate (8:2) as eluent. The purity ofthe compound was confirmed by TLC and GC-MS. ¹HNMR and ¹³CNMR spectraconfirmed the chemical identity of the metabolite as indole. (c) ¹HNMRspectrum of indole extracted from cell culture (CDCl3, 400 MHz) δ: 6.56(d, 1H, Ar C—H), 7.16 (m, 3H, Ar C—H), 7.38 (d, 1H, Ar C—H), 7.66 (d,1H, Ar C—H), 8.05 (b, 1H, Indole NH). (d) ¹³CNMR δ: 135.7, 127.8, 124.2,122, 120.7, 119.8, 111, 102.6. (e) is the ¹HNMR spectrum of pure indole.

FIG. 17. Fed batch cultivation of engineered strains in 1 L-bioreactor.Time courses of taxadiene accumulation (a), cell growth (b), acetic acidaccumulation (c) and total substrate (glycerol) addition (d) for strains22, 17 and 26 during 5 days of fed batch bioreactor cultivation in 1L-bioreactor vessels under controlled pH and oxygen conditions withminimal media and 0.5% yeast extract. After glycerol depletes to ˜0.5 to1 g/L in the fermentor, 3 g/L of glycerol was introduced into thebioreactor during the fermentation. Data are mean of two replicatebioreactors.

DETAILED DESCRIPTION OF THE INVENTION

Taxol is a potent anticancer drug first isolated as a natural productfrom the Taxus brevifolia Pacific yew tree. However, reliable andcost-efficient production of Taxol or Taxol analogs by traditionalproduction routes from plant extracts is limited. Here, we report amultivariate-modular approach to metabolic pathway engineering toamplify by ˜15000 fold the production of taxadiene in an engineeredEscherichia coli. Taxadiene, the first committed Taxol intermediate, isthe biosynthetic product of the non-mevalonate pathway in E. colicomprising two modules: the native upstream pathway forming IsopentenylPyrophosphate (IPP) and a heterologous downstream terpenoid-formingpathway. Systematic multivariate search identified conditions thatoptimally balance the two pathway modules to minimize accumulation ofinhibitory intermediates and flux diversion to side products. We alsoengineered the next step, after taxadiene, in Taxol biosynthesis, aP450-based oxidation step, that yielded >98% substrate conversion andpresent the first example of in vivo production of any functionalizedTaxol intermediates in E. coli. The modular pathway engineering approachnot only highlights the complexity of multi-step pathways, but alsoallowed accumulation of high taxadiene and taxadien-5α-ol titers (˜300mg/L and 60 mg/L, respectively) in small-scale fermentations, thusexemplifying the potential of microbial production of Taxol and itsderivatives.

This invention is not limited in its application to the details ofconstruction and the arrangement of components set forth in thefollowing description or illustrated in the drawings. The invention iscapable of other embodiments and of being practiced or of being carriedout in various ways. Also, the phraseology and terminology used hereinis for the purpose of description and should not be regarded aslimiting. The use of “including,” “comprising,” or “having,”“containing,” “involving,” and variations thereof herein, is meant toencompass the items listed thereafter and equivalents thereof as well asadditional items.

Microbial production of terpenoids such as taxadiene is demonstratedherein. When expressed at satisfactory levels, microbial routes reducedramatically the cost of production of such compounds. Additionally,they utilize cheap, abundant and renewable feedstocks (such as sugarsand other carbohydrates) and can be the source for the synthesis ofnumerous derivatives that may exhibit far superior properties than theoriginal compound. A key element in the cost-competitive production ofcompounds of the isoprenoid pathway using a microbial route is theamplification of this pathway in order to allow the overproduction ofthese molecules. Described herein are methods that enhance or amplifythe flux towards terpenoid production in Escherichia coli (E. coli).Specifically, methods are provided to amplify the metabolic flux to thesynthesis of isopentenyl pyrophosphate (IPP) (a key intermediate for theproduction of isoprenoid compounds), dimethylallyl pyrophosphate(DMAPP), geranyl diphosphate (GPP), farnesyl diphosphate (FPP),geranylgeranyl diphosphate (GGPP), and farnesyl geranyl diphosphate(FGPP), paclitaxel (Taxol), ginkolides, geraniol, farnesol,geranylgeraniol, linalool, isoprene, monoterpenoids such as menthol,carotenoids such as lycopene, polyisoprenoids such as polyisoprene ornatural rubber, diterpenoids such as eleutherobin, and sesquiterpenoidssuch as artemisinin.

Aspects of the invention relate to the production of terpenoids. As usedherein, a terpenoid, also referred to as an isoprenoid, is an organicchemical derived from a five-carbon isoprene unit. Several non-limitingexamples of terpenoids, classified based on the number of isoprene unitsthat they contain, include: hemiterpenoids (1 isoprene unit),monoterpenoids (2 isoprene units), sesquiterpenoids (3 isoprene units),diterpenoids (4 isoprene units), sesterterpenoids (5 isoprene units),triterpenoids (6 isoprene units), tetraterpenoids (8 isoprene units),and polyterpenoids with a larger number of isoprene units. In someembodiments, the terpenoid that is produced is taxadiene. In someembodiments, the terpenoid that is produced is Citronellol, Cubebol,Nootkatone, Cineol, Limonene, Eleutherobin, Sarcodictyin,Pseudopterosins, Ginkgolides, Stevioside, Rebaudioside A, sclareol,labdenediol, levopimaradiene, sandracopimaradiene or isopemaradiene.

Described herein are methods and compositions for optimizing productionof terpenoids in cells by controlling expression of genes or proteinsparticipating in an upstream pathway and a downstream pathway. Theupstream pathway involves production of isopentyl pyrophosphate (IPP)and dimethylallyl pyrophosphate (DMAPP), which can be achieved by twodifferent metabolic pathways: the mevalonic acid (MVA) pathway and theMEP (2-C-methyl-D-erythritol 4-phosphate) pathway, also called theMEP/DOXP (2-C-methyl-D-erythritol 4-phosphate/1-deoxy-D-xylulose5-phosphate) pathway, the non-mevalonate pathway or the mevalonicacid-independent pathway.

The downstream pathway is a synthetic pathway that leads to productionof a terpenoids and involves recombinant gene expression of a terpenoidsynthase (also referred to as terpene cyclase) enzyme, and ageranylgeranyl diphosphate synthase (GGPPS) enzyme. In some embodiments,a terpenoid synthase enzyme is a diterpenoid synthase enzyme. Severalnon-limiting examples of diterpenoid synthase enzymes include casbenesynthase, taxadiene synthase, levopimaradiene synthase, abietadienesynthase, isopimaradiene synthase, ent-copalyl diphosphate synthase,syn-stemar-13-ene synthase, syn-stemod-13(17)-ene synthase,syn-pimara-7,15-diene synthase, ent-sandaracopimaradiene synthase,ent-cassa-12,15-diene synthase, ent-pimara-8(14), 15-diene synthase,ent-kaur-15-ene synthase, ent-kaur-16-ene synthase, aphidicolan-16β-olsynthase, phyllocladan-16α-ol synthase, fusicocca-2,10(14)-dienesynthase, and terpentetriene cyclase.

Surprisingly, as demonstrated in the Examples section, optimization ofterpenoid synthesis by manipulation of the upstream and downstreampathways described herein, was not a simple linear or additive process.Rather, through complex combinatorial analysis, optimization wasachieved through balancing components of the upstream and downstreampathways. Unexpectedly, as demonstrated in FIGS. 1 and 2, taxadieneaccumulation exhibited a strong non-linear dependence on the relativestrengths of the upstream MEP and downstream synthetic taxadienepathways.

Aspects of the invention relate to controlling the expression of genesand proteins in the MEP pathway for optimized production of a terpenoidsuch as taxadiene. Optimized production of a terpenoid refers toproducing a higher amount of a terpenoid following pursuit of anoptimization strategy than would be achieved in the absence of such astrategy. It should be appreciated that any gene and/or protein withinthe MEP pathway is encompassed by methods and compositions describedherein. In some embodiments, a gene within the MEP pathway is one of thefollowing: dxs, ispC, ispD, ispE, ispF, ispG, ispH, idi, ispA or ispB.Expression of one or more genes and/or proteins within the MEP pathwaycan be upregulated and/or downregulated. In certain embodiments,upregulation of one or more genes and/or proteins within the MEP pathwaycan be combined with downregulation of one or more genes and/or proteinswithin the MEP pathway.

It should be appreciated that genes and/or proteins can be regulatedalone or in combination. For example, the expression of dxs can beupregulated or downregulated alone or in combination with upregulationor downregulation of expression of one or more of ispC, ispD, ispE,ispF, ispG, ispH, idi, ispA and ispB. The expression of ispC can beupregulated or downregulated alone or in combination with upregulationor downregulation of expression of one or more of dxs, ispD, ispE, ispF,ispG, ispH, idi, ispA and ispB. The expression of ispD can beupregulated or downregulated alone or in combination with upregulationor downregulation of expression of one or more of dxs, ispC, ispE, ispF,ispG, ispH, idi, ispA and ispB. The expression of ispE can beupregulated or downregulated alone or in combination with upregulationor downregulation of expression of one or more of dxs, ispC, ispD, ispF,ispG, ispH, idi, ispA and ispB. The expression of ispF can beupregulated or downregulated alone or in combination with upregulationor downregulation of expression of one or more of dxs, ispC, ispD, ispE,ispG, ispH, idi, ispA and ispB. The expression of ispG can beupregulated or downregulated alone or in combination with upregulationor downregulation of expression of one or more of dxs, ispC, ispD, ispE,ispF, ispH, idi, ispA and ispB. The expression of ispH can beupregulated or downregulated alone or in combination with upregulationor downregulation of expression of one or more of dxs, ispC, ispD, ispE,ispF, ispG, idi, ispA and ispB. The expression of idi can be upregulatedor downregulated alone or in combination with upregulation ordownregulation of expression of one or more of dxs, ispC, ispD, ispE,ispF, ispG, ispH, ispA and ispB. The expression of ispA can beupregulated or downregulated alone or in combination with upregulationor downregulation of expression of one or more of dxs, ispC, ispD, ispE,ispF, ispG, ispH, idi and ispB. The expression of ispB can beupregulated or downregulated alone or in combination with upregulationor downregulation of expression of one or more of dxs, ispC, ispD, ispE,ispF, ispG, ispH, idi and ispA. In some embodiments, expression of thegene and/or protein of one or more of dxs, ispC, ispD, ispE, ispF, ispG,ispH, and idi is upregulated while expression of the gene and/or proteinof ispA and/or ispB is downregulated.

Expression of genes within the MEP pathway can be regulated in a modularmethod. As used herein, regulation by a modular method refers toregulation of multiple genes together. For example, in some embodiments,multiple genes within the MEP pathway are recombinantly expressed on acontiguous region of DNA, such as an operon. It should be appreciatedthat a cell that expresses such a module can also express one or moreother genes within the MEP pathway either recombinantly or endogenously.

A non-limiting example of a module of genes within the MEP pathway is amodule containing the genes dxs, idi, ispD and ispF, as presented in theExamples section, and referred to herein as dxs-idi-ispDF. It should beappreciated that modules of genes within the MEP pathway, consistentwith aspects of the invention, can contain any of the genes within theMEP pathway, in any order.

Expression of genes and proteins within the downstream syntheticterpenoid synthesis pathway can also be regulated in order to optimizeterpenoid production. The synthetic downstream terpenoid synthesispathway involves recombinant expression of a terpenoid synthase enzymeand a GGPPS enzyme. Any terpenoid synthase enzyme, as discussed above,can be expressed with GGPPS depending on the downstream product to beproduced. For example, taxadiene synthase is used for the production oftaxadiene. Recombinant expression of the taxadiene synthase enzyme andthe GGPPS enzyme can be regulated independently or together. In someembodiments the two enzymes are regulated together in a modular fashion.For example the two enzymes can be expressed in an operon in eitherorder (GGPPS-TS, referred to as “GT,” or TS-GGPPS, referred to as “TG”).

Manipulation of the expression of genes and/or proteins, includingmodules such as the dxs-idi-ispDF operon, and the TS-GGPPS operon, canbe achieved through methods known to one of ordinary skill in the art.For example, expression of the genes or operons can be regulated throughselection of promoters, such as inducible promoters, with differentstrengths. Several non-limiting examples of promoters include Trc, T5and T7. Additionally, expression of genes or operons can be regulatedthrough manipulation of the copy number of the gene or operon in thecell. For example, in certain embodiments, a strain containing anadditional copy of the dxs-idi-ispDF operon on its chromosome under Trcpromoter control produces an increased amount of taxadiene relative toone overexpressing only the synthetic downstream pathway. In someembodiments, expression of genes or operons can be regulated throughmanipulating the order of the genes within a module. For example, incertain embodiments, changing the order of the genes in a downstreamsynthetic operon from GT to TG results in a 2-3 fold increase intaxadiene production. In some embodiments, expression of genes oroperons is regulated through integration of one or more genes or operonsinto a chromosome. For example, in certain embodiments, integration ofthe upstream dxs-idi-ispDF operon into the chromosome of a cell resultsin increased taxadiene production.

It should be appreciated that the genes associated with the inventioncan be obtained from a variety of sources. In some embodiments, thegenes within the MEP pathway are bacterial genes such as Escherichiacoli genes. In some embodiments, the gene encoding for GGPPS is a plantgene. For example, the gene encoding for GGPPS can be from a species ofTaxus such as Taxus canadensis (T. canadensis). In some embodiments, thegene encoding for taxadiene synthase is a plant gene. For example, thegene encoding for taxadiene synthase can be from a species of Taxus suchas Taxus brevifolia (T. brevifolia). Representative GenBank Accessionnumbers for T. canadensis GGPPS and T. brevifolia taxadiene synthase areprovided by AF081514 and U48796, the sequences of which are incorporatedby reference herein in their entireties.

As one of ordinary skill in the art would be aware, homologous genes foruse in methods associated with the invention can be obtained from otherspecies and can be identified by homology searches, for example througha protein BLAST search, available at the National Center forBiotechnology Information (NCBI) internet site (www.ncbi.nlm.nih.gov).Genes and/or operons associated with the invention can be cloned, forexample by PCR amplification and/or restriction digestion, from DNA fromany source of DNA which contains the given gene. In some embodiments, agene and/or operon associated with the invention is synthetic. Any meansof obtaining a gene and/or operon associated with the invention iscompatible with the instant invention.

In some embodiments, further optimization of terpenoid production isachieved by modifying a gene before it is recombinantly expressed in acell. In some embodiments, the GGPPS enzyme has one or more of thefollow mutations: A162V, G140C, L182M, F218Y, D160G, C184S, K367R,A151T, M185I, D264Y, E368D, C184R, L331I, G262V, R365S, A114D, S239C,G295D, I276V, K343N, P183S, I172T, D267G, I149V, T234I, E153D and T259A.In some embodiments, the GGPPS enzyme has a mutation in residue S239and/or residue G295. In certain embodiments, the GGPPS enzyme has themutation S239C and/or G295D.

In some embodiments, modification of a gene before it is recombinantlyexpressed in a cell involves codon optimization for expression in abacterial cell. Codon usages for a variety of organisms can be accessedin the Codon Usage Database (www.kazusa.or.jp/codon/). Codonoptimization, including identification of optimal codons for a varietyof organisms, and methods for achieving codon optimization, are familiarto one of ordinary skill in the art, and can be achieved using standardmethods.

In some embodiments, modifying a gene before it is recombinantlyexpressed in a cell involves making one or more mutations in the genebefore it is recombinantly expressed in a cell. For example, a mutationcan involve a substitution or deletion of a single nucleotide ormultiple nucleotides. In some embodiments, a mutation of one or morenucleotides in a gene will result in a mutation in the protein producedfrom the gene, such as a substitution or deletion of one or more aminoacids.

In some embodiments, it may be advantageous to use a cell that has beenoptimized for production of a terpenoid. For example, in someembodiments, a cell that overexpresses one or more components of thenon-mevalonate (MEP) pathway is used, at least in part, to amplifyisopentyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP),substrates of GGPPS. In some embodiments, overexpression of one or morecomponents of the non-mevalonate (MEP) pathway is achieved by increasingthe copy number of one or more components of the non-mevalonate (MEP)pathway. For example, copy numbers of components at rate-limiting stepsin the MEP pathway such as (dxs, ispD, ispF, idi) can be amplified, suchas by additional episomal expression.

In some embodiments “rational design” is involved in constructingspecific mutations in proteins such as enzymes. As used herein,“rational design” refers to incorporating knowledge of the enzyme, orrelated enzymes, such as its three dimensional structure, its activesite(s), its substrate(s) and/or the interaction between the enzyme andsubstrate, into the design of the specific mutation. Based on a rationaldesign approach, mutations can be created in an enzyme which can then bescreened for increased production of a terpenoid relative to controllevels. In some embodiments, mutations can be rationally designed basedon homology modeling. As used herein, “homology modeling” refers to theprocess of constructing an atomic resolution model of one protein fromits amino acid sequence and a three-dimensional structure of a relatedhomologous protein.

In some embodiments, random mutations can be made in a gene, such as agene encoding for an enzyme, and these mutations can be screened forincreased production of a terpenoid relative to control levels. Forexample, screening for mutations in components of the MEP pathway, orcomponents of other pathways, that lead to enhanced production of aterpenoid may be conducted through a random mutagenesis screen, orthrough screening of known mutations. In some embodiments, shotguncloning of genomic fragments could be used to identify genomic regionsthat lead to an increase in production of a terpenoid, through screeningcells or organisms that have these fragments for increased production ofa terpenoid. In some cases one or more mutations may be combined in thesame cell or organism.

In some embodiments, production of a terpenoid in a cell can beincreased through manipulation of enzymes that act in the same pathwayas the enzymes associated with the invention. For example, in someembodiments it may be advantageous to increase expression of an enzymeor other factor that acts upstream of a target enzyme such as an enzymeassociated with the invention. This could be achieved by over-expressingthe upstream factor using any standard method.

Optimization of protein expression can also be achieved throughselection of appropriate promoters and ribosome binding sites. In someembodiments, this may include the selection of high-copy numberplasmids, or low or medium-copy number plasmids. The step oftranscription termination can also be targeted for regulation of geneexpression, through the introduction or elimination of structures suchas stem-loops.

Aspects of the invention relate to expression of recombinant genes incells. The invention encompasses any type of cell that recombinantlyexpresses genes associated with the invention, including prokaryotic andeukaryotic cells. In some embodiments the cell is a bacterial cell, suchas Escherichia spp., Streptomyces spp., Zymonas spp., Acetobacter spp.,Citrobacter spp., Synechocystis spp., Rhizobium spp., Clostridium spp.,Corynebacterium spp., Streptococcus spp., Xanthomonas spp.,Lactobacillus spp., Lactococcus spp., Bacillus spp., Alcaligenes spp.,Pseudomonas spp., Aeromonas spp., Azotobacter spp., Comamonas spp.,Mycobacterium spp., Rhodococcus spp., Gluconobacter spp., Ralstoniaspp., Acidithiobacillus spp., Microlunatus spp., Geobacter spp.,Geobacillus spp., Arthrobacter spp., Flavobacterium spp., Serratia spp.,Saccharopolyspora spp., Thermus spp., Stenotrophomonas spp.,Chromobacterium spp., Sinorhizobium spp., Saccharopolyspora spp.,Agrobacterium spp. and Pantoea spp. The bacterial cell can be aGram-negative cell such as an Escherichia coli (E. coli) cell, or aGram-positive cell such as a species of Bacillus. In other embodiments,the cell is a fungal cell such as a yeast cell, e.g., Saccharomycesspp., Schizosaccharomyces spp., Pichia spp., Paffia spp., Kluyveromycesspp., Candida spp., Talaromyces spp., Brettanomyces spp., Pachysolenspp., Debaryomyces spp., Yarrowia spp., and industrial polyploid yeaststrains. Preferably the yeast strain is a S. cerevisiae strain or aYarrowia spp. strain. Other examples of fungi include Aspergillus spp.,Pennicilium spp., Fusarium spp., Rhizopus spp., Acremonium spp.,Neurospora spp., Sordaria spp., Magnaporthe spp., Allomyces spp.,Ustilago spp., Botrytis spp., and Trichoderma spp. In other embodiments,the cell is an algal cell, or a plant cell. It should be appreciatedthat some cells compatible with the invention may express an endogenouscopy of one or more of the genes associated with the invention as wellas a recombinant copy. In some embodiments, if a cell has an endogenouscopy of one or more of the genes associated with the invention then themethods will not necessarily require adding a recombinant copy of thegene(s) that are endogenously expressed. In some embodiments the cellmay endogenously express one or more enzymes from the pathways describedherein and may recombinantly express one or more other enzymes from thepathways described herein for efficient production of a terpenoid.

Further aspects of the invention relate to screening for bacterial cellsor strains that exhibit optimized terpenoid production. As describedabove, methods associated with the invention involve generating cellsthat overexpress one or more genes in the MEP pathway. Terpenoidproduction from culturing of such cells can be measured and compared toa control cell wherein a cell that exhibits a higher amount of aterpenoid production relative to a control cell is selected as a firstimproved cell. The cell can be further modified by recombinantexpression of a terpenoid synthase enzyme and a GGPPS enzyme. The levelof expression of one or more of the components of the non-mevalonate(MEP) pathway, the terpenoid synthase enzyme and/or the GGPPS enzyme inthe cell can then be manipulated and terpenoid production can bemeasured again, leading to selection of a second improved cell thatproduces greater amounts of a terpenoid than the first improved cell. Insome embodiments, the terpenoid synthase enzyme is a taxadiene synthaseenzyme.

Further aspects of the invention relate to the identification andcharacterization (via GC-MS) of a previously unknown metabolite inbacterial E. coli cells (FIGS. 3 and 6). The level of accumulation ofthe newly identified metabolite, indole, can be controlled bygenetically manipulating the microbial pathway by the overexpression,down regulation or mutation of the isoprenoid pathway genes. Themetabolite indole anti-correlates as a direct variable to the taxadieneproduction in engineered strains (FIGS. 3, 6 and 15). Furthercontrolling the accumulation of indole for improving the flux towardsterpenoid biosynthesis in bacterial systems (specifically in cells, suchas E. coli cells) or other cells, can be achieved by balancing theupstream non-mevalonate isoprenoid pathway with the downstream productsynthesis pathways or by modifications to or regulation of the indolepathway. In so doing, the skilled person can reduce or control theaccumulation of indole and thereby reduce the inhibitory effect ofindole on the production of taxadiene, and other terpenoids derived fromthe described pathways, such as: monoterpenoids, sesquiterpenoids(including amorphadiene), diterpenoids (including levopimaradiene),triterpenes, and tetraterpenes. Other methods for reducing orcontrolling the accumulation of indole include removing the accumulatedindole from the fermentation through chemical methods such as by usingabsorbents, scavengers, etc.

In other embodiments, methods are provided that include measuring theamount or concentration of indole in a cell that produces one or moreterpenoids or in a culture of the cells that produce one or moreterpenoids. The amount or concentration of indole can be measured once,or two or more times, as suitable, using methods known in the art and asdescribed herein. Such methods can be used to guide processes ofproducing one or more terpenoids, e.g., in process improvement. Suchmethods can be used to guide strain construction, e.g., for strainimprovement.

The identification of the means to achieve this balancing yielded a15000 fold improvement in the overproduction of terpenoids such astaxadiene, compared to wild type bacterial cells, expressed with aheterologous taxadiene biosynthetic pathway. The production was furtherincreased through modified fermentation methods that yieldedconcentrations of approximately 2 g/L, which is 1500 fold highercompared to any prior reported taxadiene production. As demonstratedherein, by genetically engineering the non-mevalonate isoprenoid pathwayin E. coli the accumulation of this metabolite can now be controlledwhich regulates the flux towards the isoprenoid biosynthesis inbacterial E. coli cells. Also demonstrated herein is further channelingof the taxadiene production into the next key precursor to Taxol,taxadien-5α-ol, achieved through engineering the oxidation chemistry forTaxol biosynthesis. Example 5 presents the first successful extension ofthe synthetic pathway from taxadiene to taxadien-5α-ol. Similar to themajority of other terpenoids, the Taxol biosynthesis follows the unifiedfashion of “two phase” biosynthetic process, (i) the “cyclase phase” oflinear coupling of the prenyl precursors (IPP and DMAPP) to GGPPfollowed by the molecular cyclization and rearrangement for thecommitted precursor taxadiene (FIG. 6, VIII-IX).^(57,58) After thecommitted precursor, (ii) the “oxidation phase”, the cyclic olefintaxadiene core structure is then functionalized by seven cytochrome P450oxygenases together with its redox partners, decorated with two acetategroups and a benzoate group by acyl and aroyl CoA-dependenttransferases, keto group by keto-oxidase, and epoxide group by epoxidaselead to the late intermediate baccatin III, to which the C13 side chainis attached for Taxol ((FIG. 6, X-XIII).¹⁵ Although a rough sequentialorder of the early oxidation phase reactions are predicted, the precisetiming/order of some of the hydroxylations, acylations and benzoylationreactions are uncertain. However it is clear that the early bifurcationstarts from the cytochrome p450 mediated hydroxylation of taxadiene coreat C5 position followed the downstream hydroxylations using a homologousfamily of cytochrome p450 enzymes with high deduced similarity to eachother (>70%) but with limited resemblance (<30%) to other plantp450's.^(41,59) In addition, the structural and functional diversitywith the possible evolutionary analysis implicit that thetaxadiene-5α-ol gene can be the parental sequence from which the otherhydroxylase genes in the Taxol biosynthetic pathway evolved, reflectingthe order of hydroxylations.¹⁵

Further aspects of the invention relate to chimeric P450 enzymes.Functional expression of plant cytochrome P450 has been consideredchallenging due to the inherent limitations of bacterial platforms, suchas the absence of electron transfer machinery, cytochrome P450reductases, and translational incompatibility of the membrane signalmodules of P450 enzymes due to the lack of an endoplasmic reticulum.

In some embodiments, the taxadiene-5α-hydroxylase associated withmethods of the invention is optimized through N-terminal transmembraneengineering and/or the generation of chimeric enzymes throughtranslational fusion with a CPR redox partner. In some embodiments, theCPR redox partner is a Taxus cytochrome P450 reductase (TCPR; FIG. 5 b).In certain embodiments, cytochrome P450 taxadiene-5α-hydroxylase (T5αOH)is obtained from Taxus cuspidate (GenBank Accession number AY289209, thesequence of which is incorporated by reference herein). In someembodiments, NADPH:cytochrome P450 reductase (TCPR) is obtained fromTaxus cuspidate (GenBank Accession number AY571340, the sequence ofwhich is incorporated by reference herein).

The taxadiene 5α-hydroxylase and TCPR can be joined by a linker such asGSTGS (SEQ ID NO:50). In some embodiments, taxadiene 5α-hydroxylaseand/or TCPR are truncated to remove all or part of the transmembraneregion of one or both proteins. For example, taxadiene 5α-hydroxylase insome embodiments is truncated to remove 8, 24, or 42 N-terminal aminoacids. In some embodiments, the N-terminal 74 amino acids of TCPR aretruncated. An additional peptide can also be fused to taxadiene5α-hydroxylase. For example, one or more amino acids from bovine 17αhydroxylase can be added to taxadiene 5α-hydroxylase. In certainembodiments, the peptide MALLLAVF (SEQ ID NO:51) is added to taxadiene5α-hydroxylase. A non-limiting example of polypeptide comprisingtaxadiene 5α-hydroxylase fused to TCPR is At24T5αOH-tTCPR.

In some embodiments, the chimeric enzyme is able to carry out the firstoxidation step with more than 10% taxadiene conversion totaxadiene-5α-ol and the byproduct 5(12)-Oxa-3(11)-cyclotaxane. Forexample, the percent taxadiene conversion to taxadiene-5α-ol and thebyproduct 5(12)-Oxa-3(11)-cyclotaxane can be at least 20%, at least 30%,at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 95%, at least 98%, approximately 99% orapproximately 100%.

In certain embodiments, the chimeric enzyme is At245αOH-tTCPR, which wasfound to be capable of carrying out the first oxidation step with morethan 98% taxadiene conversion to taxadiene-5α-ol and the byproduct5(12)-Oxa-3(11)-cyclotaxane (OCT; FIG. 9 a). Engineering of the step oftaxadiene-5α-ol production is critical in the production of Taxol andwas found to be limiting in previous efforts to construct this pathwayin yeast. The engineered construct developed herein demonstrated greaterthan 98% conversion of taxadiene in vivo with a 2400 fold improvementover previous heterologous expression in yeast. Thus, in addition tosynthesizing significantly greater amounts of key Taxol intermediates,this study also provides the basis for the synthesis of subsequentmetabolites in the pathway by similar P450 chemistry.

As used herein, the terms “protein” and “polypeptide” are usedinterchangeably and thus the term polypeptide may be used to refer to afull-length polypeptide and may also be used to refer to a fragment of afull-length polypeptide. As used herein with respect to polypeptides,proteins, or fragments thereof, “isolated” means separated from itsnative environment and present in sufficient quantity to permit itsidentification or use. Isolated, when referring to a protein orpolypeptide, means, for example: (i) selectively produced by expressioncloning or (ii) purified as by chromatography or electrophoresis.Isolated proteins or polypeptides may be, but need not be, substantiallypure. The term “substantially pure” means that the proteins orpolypeptides are essentially free of other substances with which theymay be found in production, nature, or in vivo systems to an extentpractical and appropriate for their intended use. Substantially purepolypeptides may be obtained naturally or produced using methodsdescribed herein and may be purified with techniques well known in theart. Because an isolated protein may be admixed with other components ina preparation, the protein may comprise only a small percentage byweight of the preparation. The protein is nonetheless isolated in thatit has been separated from the substances with which it may beassociated in living systems, i.e. isolated from other proteins.

The invention also encompasses nucleic acids that encode for any of thepolypeptides described herein, libraries that contain any of the nucleicacids and/or polypeptides described herein, and compositions thatcontain any of the nucleic acids and/or polypeptides described herein.

In some embodiments, one or more of the genes associated with theinvention is expressed in a recombinant expression vector. As usedherein, a “vector” may be any of a number of nucleic acids into which adesired sequence or sequences may be inserted by restriction andligation for transport between different genetic environments or forexpression in a host cell. Vectors are typically composed of DNA,although RNA vectors are also available. Vectors include, but are notlimited to: plasmids, fosmids, phagemids, virus genomes and artificialchromosomes.

A cloning vector is one which is able to replicate autonomously orintegrated in the genome in a host cell, and which is furthercharacterized by one or more endonuclease restriction sites at which thevector may be cut in a determinable fashion and into which a desired DNAsequence may be ligated such that the new recombinant vector retains itsability to replicate in the host cell. In the case of plasmids,replication of the desired sequence may occur many times as the plasmidincreases in copy number within the host cell such as a host bacteriumor just a single time per host before the host reproduces by mitosis. Inthe case of phage, replication may occur actively during a lytic phaseor passively during a lysogenic phase.

An expression vector is one into which a desired DNA sequence may beinserted by restriction and ligation such that it is operably joined toregulatory sequences and may be expressed as an RNA transcript. Vectorsmay further contain one or more marker sequences suitable for use in theidentification of cells which have or have not been transformed ortransfected with the vector. Markers include, for example, genesencoding proteins which increase or decrease either resistance orsensitivity to antibiotics or other compounds, genes which encodeenzymes whose activities are detectable by standard assays known in theart (e.g., β-galactosidase, luciferase or alkaline phosphatase), andgenes which visibly affect the phenotype of transformed or transfectedcells, hosts, colonies or plaques (e.g., green fluorescent protein).Preferred vectors are those capable of autonomous replication andexpression of the structural gene products present in the DNA segmentsto which they are operably joined.

As used herein, a coding sequence and regulatory sequences are said tobe “operably” joined when they are covalently linked in such a way as toplace the expression or transcription of the coding sequence under theinfluence or control of the regulatory sequences. If it is desired thatthe coding sequences be translated into a functional protein, two DNAsequences are said to be operably joined if induction of a promoter inthe 5′ regulatory sequences results in the transcription of the codingsequence and if the nature of the linkage between the two DNA sequencesdoes not (1) result in the introduction of a frame-shift mutation, (2)interfere with the ability of the promoter region to direct thetranscription of the coding sequences, or (3) interfere with the abilityof the corresponding RNA transcript to be translated into a protein.Thus, a promoter region would be operably joined to a coding sequence ifthe promoter region were capable of effecting transcription of that DNAsequence such that the resulting transcript can be translated into thedesired protein or polypeptide.

When the nucleic acid molecule that encodes any of the enzymes of theclaimed invention is expressed in a cell, a variety of transcriptioncontrol sequences (e.g., promoter/enhancer sequences) can be used todirect its expression. The promoter can be a native promoter, i.e., thepromoter of the gene in its endogenous context, which provides normalregulation of expression of the gene. In some embodiments the promotercan be constitutive, i.e., the promoter is unregulated allowing forcontinual transcription of its associated gene. A variety of conditionalpromoters also can be used, such as promoters controlled by the presenceor absence of a molecule.

The precise nature of the regulatory sequences needed for geneexpression may vary between species or cell types, but shall in generalinclude, as necessary, 5′ non-transcribed and 5′ non-translatedsequences involved with the initiation of transcription and translationrespectively, such as a TATA box, capping sequence, CAAT sequence, andthe like. In particular, such 5′ non-transcribed regulatory sequenceswill include a promoter region which includes a promoter sequence fortranscriptional control of the operably joined gene. Regulatorysequences may also include enhancer sequences or upstream activatorsequences as desired. The vectors of the invention may optionallyinclude 5′ leader or signal sequences. The choice and design of anappropriate vector is within the ability and discretion of one ofordinary skill in the art.

Expression vectors containing all the necessary elements for expressionare commercially available and known to those skilled in the art. See,e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, SecondEdition, Cold Spring Harbor Laboratory Press, 1989. Cells aregenetically engineered by the introduction into the cells ofheterologous DNA (RNA). That heterologous DNA (RNA) is placed underoperable control of transcriptional elements to permit the expression ofthe heterologous DNA in the host cell. Heterologous expression of genesassociated with the invention, for production of a terpenoid, such astaxadiene, is demonstrated in the Examples section using E. coli. Thenovel method for producing terpenoids can also be expressed in otherbacterial cells, fungi (including yeast cells), plant cells, etc.

A nucleic acid molecule that encodes an enzyme associated with theinvention can be introduced into a cell or cells using methods andtechniques that are standard in the art. For example, nucleic acidmolecules can be introduced by standard protocols such as transformationincluding chemical transformation and electroporation, transduction,particle bombardment, etc. Expressing the nucleic acid molecule encodingthe enzymes of the claimed invention also may be accomplished byintegrating the nucleic acid molecule into the genome.

In some embodiments one or more genes associated with the invention isexpressed recombinantly in a bacterial cell. Bacterial cells accordingto the invention can be cultured in media of any type (rich or minimal)and any composition. As would be understood by one of ordinary skill inthe art, routine optimization would allow for use of a variety of typesof media. The selected medium can be supplemented with variousadditional components. Some non-limiting examples of supplementalcomponents include glucose, antibiotics, IPTG for gene induction, ATCCTrace Mineral Supplement, and glycolate. Similarly, other aspects of themedium, and growth conditions of the cells of the invention may beoptimized through routine experimentation. For example, pH andtemperature are non-limiting examples of factors which can be optimized.In some embodiments, factors such as choice of media, media supplements,and temperature can influence production levels of terpenoids, such astaxadiene. In some embodiments the concentration and amount of asupplemental component may be optimized. In some embodiments, how oftenthe media is supplemented with one or more supplemental components, andthe amount of time that the media is cultured before harvesting aterpenoid, such as taxadiene, is optimized.

According to aspects of the invention, high titers of a terpenoid suchas taxadiene, are produced through the recombinant expression of genesassociated with the invention, in a cell. As used herein “high titer”refers to a titer in the milligrams per liter (mg L⁻¹) scale. The titerproduced for a given product will be influenced by multiple factorsincluding choice of media. In some embodiments, the total taxadienetiter is at least 1 mg L⁻¹. In some embodiments, the total taxadienetiter is at least 10 mg L⁻¹. In some embodiments, the total taxadienetiter is at least 250 mg L⁻¹. For example, the total taxadiene titer canbe at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 75,80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350,375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700,725, 750, 775, 800, 825, 850, 875, 900 or more than 900 mg L⁻¹ includingany intermediate values. In some embodiments, the total taxadiene titercan be at least 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0,2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4,3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8,4.9, 5.0, or more than 5.0 g L⁻¹ including any intermediate values.

In some embodiments, the total taxadiene 5α-ol titer is at least 1 mgL⁻¹. In some embodiments, the total taxadiene 5α-ol titer is at least 10mg L⁻¹. In some embodiments, the total taxadiene 5α-ol titer is at least50 mg L⁻¹. For example, the total taxadiene 5α-ol titer can be at least1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56,57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, or more than 70mg L⁻¹ including any intermediate values.

The liquid cultures used to grow cells associated with the invention canbe housed in any of the culture vessels known and used in the art. Insome embodiments large scale production in an aerated reaction vesselsuch as a stirred tank reactor can be used to produce large quantitiesof terpenoids, such as taxadiene, that can be recovered from the cellculture. In some embodiments, the terpenoid is recovered from the gasphase of the cell culture, for example by adding an organic layer suchas dodecane to the cell culture and recovering the terpenoid from theorganic layer.

Terpenoids, such as taxadiene, produced through methods described hereinhave widespread applications including pharmaceuticals such aspaclitaxel (Taxol), artemisinin, ginkolides, eleutherobin andpseudopterosins, and many other potential pharmaceutical compounds.Further applications include compounds used in flavors and cosmeticssuch as geraniol, farnesol, geranlygeraniol, linalool, limonene, pinene,cineol and isoprene. Further applications include compounds for use asbiofuels such as alcohols of 5, 10, and 15 carbon atom length. It isnoted that the above compounds are presently produced as extracts ofvarious plants. Plant extract-based methods are tedious, yield verysmall amounts and are limited as to the actual molecules that can be soobtained, namely, they do not allow the easy production of derivativesthat may possess far superior properties than the original compounds.

EXAMPLES

Methods

Strains, Plasmids, Oligonucleotides and Genes

E. coli K12 MG1655 strain was used as the host strain of all thetaxadiene strain construction. E coli K12MG1655 Δ(recA,endA) and E coliK12MG1655Δ(recA,endA)ED3 strains were provided by Professor KristalaPrather's lab at MIT (Cambridge, Mass.). Detail of all the plasmidsconstructed for the study is shown in Table 2. All oligonucleotides usedin this study are contained in Table 3.

The sequences of geranylgeranyl pyrophosphate synthase (GGPPS),⁵⁰Taxadiene synthase (TS),⁵¹ Cytochrome P450 Taxadiene 5α-hydroxylase(T5αOH) and Taxus NADPH:cytochrome P450 reductase (TCPR)⁴⁶ were obtainedfrom Taxus canadensis, Taxus brevifolia, Taxus cuspidate (Genbankaccession codes: AF081514, U48796, AY289209 and AY571340). Genes werecustom-synthesized using the plasmids and protocols reported by Kodumalet al.⁵² (Supplementary details Appendix 1) to incorporate E. colitranslation codon and removal of restriction sites for cloning purposes.Nucleotides corresponding to the 98 and 60 N-terminal amino acids ofGGPPS and TS (plastid transit peptide) were removed and the translationinsertion sequence Met was inserted.¹⁷

Construction of MEP Pathway (dxs-idi-idpDF Operon).

dxs-idi-ispDF operon was initially constructed by cloning each of thegenes from the genome of E coli K12 MG1655 using the primers dxs(s),dxs(a), idi(s), idi(a), ispDF(s) and ispDFI(a) under pET21C+ plasmidwith T7 promoter (p20T7MEP).⁵³ Using the primers dxsidiispDFNcoI (s) anddxsidiispDFKpnI(a) dxs-idi-ispDF operon was sub-cloned into andpTrcHis2B (Invitrogen) plasmid after digested with NcoI and KpnI forpTrcMEP plasmid (p20TrcMEP). p20TrcMEP plasmid digested with M1uI andPmeI and cloned into M1uI and PmeI digested pACYC184-melA(P2A) plasmidto construct p10TrcMEP plasmid. pTrcMEP plasmid digested with BstZ17Iand ScaI and cloned into PvuII digested pCL1920 plasmid to constructp5TrcMEP plasmid. For constructing p20T5MEP plasmid initially thedxs-idi-ispDF operon was cloned into pQE plasmid with T5 promoter(pQE-MEP) using the primers dxsidiispDFNcoI (s) and dxsidiispDFXhoI(a).A fraction of the operon DNA with T5 promoter was amplified using theprimers T5AgeI(s) and T5NheI(a) from pQEMEP plasmid. The DNA fragmentwas digested with AgeI/NheI and cloned into the p20T7MEP plasmiddigested with SGrAI/NheI enzymes.

Construction of Taxadiene Pathway (GT and TG Operons).

The downstream taxadiene pathways (GT and TG operon) were constructed bycloning PCR fragments of GGPS and TS into the NocI-EcoRI and EcoRI-SalIsites of pTrcHIS2B plasmid to create p20TrcGT and p20TrcTG using theprimers GGPPSNcoI(s), GGPPSEcoRI(a), TSEcoRI(s), TSsalI(a), TSNcoI(s)TSEcoRI(a) GGPPSEcoRI(s) and GGPPSSalI(a). For constructing p20T5GT,initially the operon was amplified with primers GGPPSNcoI(s) andTSXhoI(a) and cloned into a pQE plasmid under T5 promoter digested withNcoI/XhoI. Further the sequence was digested with XbaI and XhoI andcloned into the pTrc plasmid backbone amplified using the primerspTrcSal(s) and pTrcXba(a). p10T7TG was constructed by subcloning theNcoI/SalI digested TG operon from p20TrcTG into NcoI/SalI digestedpACYC-DUET1 plasmid. p5T7TG was constructed by cloning the BspEI/XbaIdigested fragment to the XbaI/BspEI digested DNA amplified from pCL1920plasmid using pCLBspEI(s) and pCLXbaI(a) primers.

Construction of Chromosomal Integration MEP Pathway Plasmids

For constructing the plasmids with FRP-Km-FRP cassette for amplifyingthe sequence for integration, p20T7MEP and p20T5MEP was digested withXhoI/ScaI. FRP-Km-FRP cassette was amplified from the Km cassette withFRP sequence from pkD13 plasmid using the primers KmFRPXhoI(s) andKmFRPScaI(a). The amplified DNA was digested with XhoI/ScaI and clonedinto the XhoI/ScaI digested p20T7MEP and p20T5MEP plasmid (p20T7MEPKmFRPand p20T5MEPKmFRP). Similarly the p20TrcMEP plasmid was digested withSacI/ScaI and the amplified DNA using the primers KmFRPSacI(s) andKmFRPScaI(a) was digested, cloned into the p20TrcMEP plasmid(p20TrcMEPKm-FRP).

Chromosomal Integration of the MEP Pathway Cassette(LacIq-MEP-FRP-Km-FRP) Cassette

The MEP pathways constructed under the promoters T7, T5 and Trc werelocalized to the ara operon region in the chromosome with the Kanmarker. The PCR fragments were amplified from p20T7MEPKmFRP,p20T5MEPKmFRP and p20TrcMEPKm-FRP using the primers IntT7T5(s),IntTrc(s) and Int(a) and then electroporated into E. coil MG1655recA-end- and E. coli MG1655 recA-end- EDE3 cells for chromosomalintegration through the λ Red recombination technique.⁵⁴ The sitespecific localization was confirmed and the Km marker was removedthrough the action of the FLP recombinase after successful geneintegration.

Construction of Taxadiene 5α-ol Pathway

The transmembrane region (TM) of the taxadiene 5α-ol hydroxylase (T5αOH)and Taxus Cytochrome P450 reductase (TCPR) was identified usingPredictProtein software (www.predictprotein.org).⁵⁵ For transmembraneengineering selective truncation at 8, 24 and 42 amino acid residues onthe N-terminal transmembrane region of taxadiene 5α-ol hydroxylase(T5αOH) and 74 amino acid region in the TCPR was performed. The removalof the 8, 24 and 42 residue N-terminal amino acids of taxadiene 5α-olhydroxylase (T5αOH), incorporation of one amino acid substituted bovine17α hydroxylase N-terminal 8 residue peptide MALLLAVF (SEQ ID NO:51) tothe N-terminal truncated T5αOH sequences⁴⁴ and GSTGS peptide linker wascarried out using the primer CYP17At8AANdeI(s), CYP17At24AANdeI(s),CYP17At42AANdeI(s) and CYPLinkBamHI(a). Using these primers eachmodified DNA was amplified, NdeI/BamHI digested and cloned intoNdeI/BamHI digested pACYC DUET1 plasmid to construct p10At8T5αOH,p10At24T5αOH and p10At42T5αOH plasmids. 74 amino acid truncated TCPR(tTCPR) sequence was amplified using primers CPRBamHI(s) and CPRSalI(a).The amplified tTCPR sequence and the plasmids, p10At8T5αOH, p10At24T5αOHand p10At42T5αOH, was digested with BamHI/SalI and cloned to constructthe plasmids p10At8T5αOH-tTCPR, p10At24T5αOH-tTCPR andp10At42T5αOH-tTCPR.

Culture Growth for Screening the Taxadiene and Taxadiene-5α-ol Analysis

Single transformants of pre-engineered E. coli strains harboring theappropriate plasmid with upstream (MEP), downstream taxadiene pathwayand taxadiene 5α-ol were cultivated for 18 h at 30° C. in Luria-Bertani(LB) medium (supplemented with appropriate antibiotics, 100 mg/mLcarbenecilin, 34 mg/mL chloramphenicol, 25 mg/L kanamycin or 50 mg/Lspectinomycin). For small scale cultures to screen the engineeredstrains, these preinnoculum were used to seed fresh 2-mL rich media (5g/L yeast extract, 10 g/L Trypton, 15 g/L, glucose, 10 g/L NaCl, 100 mMHEPS, 3 mL/L Antifoam B, pH 7.6, 100 ug/mL Carbenicillin and 34 ug/mLchloramphenicol), at a starting A₆₀₀ of 0.1. The culture was maintainedwith appropriate antibiotics and 100 mM IPTG for gene induction at 22°C. for 5 days.

Bioreactor Experiments for the Taxadiene 5α-ol Producing Strain.

The 3-L Bioflo bioreactor (New Brunswick) was assembled as tomanufacturer's instructions. One liter of rich media with 1% glycerol(v/v) was inoculated with 50 mL of 8 h culture (A₆₀₀ of ˜2.2) of thestrain 26-At24T5αOH-tTCPR grown in LB medium containing the antibiotics(100 mg/mL carbenicillin, 34 mg/mL chloramphenicol) at the sameconcentrations. 1 L-bioreactors with biphasic liquid-liquid fermentationusing 20% v/v dodecane. Oxygen was supplied as filtered air at 0.5 v/v/mand agitation was adjusted to maintain dissolved oxygen levels above50%. pH of the culture was controlled at 7.0 using 10% NaOH. Thetemperature of the culture in the fermentor was controlled at 30° C.until the cells were grown into an optical density of approximately 0.8,as measured at a wavelength of 600 nm (OD600). The temperature of thefermentor was reduced to 22° C. and the cells were induced with 0.1 mMIPTG. Dodecane was added aseptically to 20% (v/v) of the media volume.During the course of the fermentation the concentration of glycerol andacetate accumulation was monitored with constant time intervals. Duringthe fermentation as the glycerol concentration depleted below 0.5 g/L,glycerol (3 g/L) was introduced into the bioreactor.

The fermentation was further optimized using a fed batch cultivationwith a defined feed medium containing 0.5% yeast extract and 20% (v/v)dodecane (13.3 g/L KH₂PO₄, 4 g/L (NH₄)₂HPO₄, 1.7 g/L citric acid, 0.0084g/L EDTA, 0.0025 g/L CoCl₂, 0.015 g/L MnCl₂, 0.0015 g/L CuCl₂, 0.003 g/LH₃BO₃, 0.0025 g/L Na₂MoO₄, 0.008 g/L Zn(CH₃COO)₂, 0.06 g/L Fe(III)citrate, 0.0045 g/L thiamine, 1.3 g/L MgSO₄, 10 g/L glycerol, 5 g/Lyeast extract, pH 7.0). The same medium composition was used for thefermentation of strains 17 and 26 with appropriate antibiotics (strain17: 100 μg/mL carbenicillin and 50 μg/mL spectinomycin; strain 26: 50μg/mL spectinomycin).

For the taxadien-5α-ol producing strain, one liter of complex mediumwith 1% glycerol (v/v) was inoculated with 50 mL of an 8 h culture (ODof ˜2.2) of strain 26-At24T5αOH-tTCPR grown in LB medium containing 50μg/mL spectinomycin and 34 μg/mL chloramphenicol). Oxygen was suppliedas filtered air at 0.5 (vvm) and agitation was adjusted to maintaindissolved oxygen levels above 30%. The pH of the culture was controlledat 7.0 using 10% NaOH. The temperature of the culture in the fermentorwas controlled at 30° C. until the cells were grown into an opticaldensity of approximately 0.8, as measured at a wavelength of 600 nm(OD600). The temperature of the fermentor was reduced to 22° C. and thepathway was induced with 0.1 mM IPTG. Dodecane was added aseptically to20% (v/v) of the media volume. During the course of the fermentation,the concentration of glycerol and acetate accumulation was monitoredwith constant time intervals. During the fermentation as the glycerolconcentration depleted 0.5-1 g/L, 3 g/L of glycerol was introduced intothe bioreactor.

GC-MS Analysis of Taxadiene and Taxadiene-5α-ol

For analysis of taxadiene accumulation from small scale culture, 1.5 mLof the culture was vortexed with 1 mL hexane for 30 min. The mixture wascentrifuged to separate the organic layer. For bioreactor 1 uL of thedodecane layer was diluted to 200 uL using hexane. 1 uL of the hexanelayer was analyzed by GC-MS (Varian saturn 3800 GC attached to a Varian2000 MS). The sample was injected into a HP5ms column (30 m×250 uM×0.25uM thickness) (Agilent Technologies USA). Helium (ultra purity) at aflow rate 1.0 ml/min was used as a carrier gas. The oven temperature wasfirst kept constant at 50° C. for 1 min, and then increased to 220° C.at the increment of 10° C./min, and finally held at this temperature for10 min. The injector and transfer line temperatures were set at 200° C.and 250° C., respectively.

Standard compounds from biological or synthetic sources for taxadieneand taxadiene 5α-ol was not commercially available. Thus we performedfermentations of taxadiene producing E. coli in a 2 L bioreactor toextract pure material. Taxadiene was extracted by solvent extractionusing hexane, followed by multiple rounds of silica columnchromatography to obtain the pure material for constructing a standardcurve for GC-MS analysis. We have compared the GC and MS profile of thepure taxadiene with the reported literature to confirm the authenticityof the compound⁶⁰. In order to check the purity we have performed 1HNMRof taxadiene. Since the accumulation of taxadiene-5α-ol was very lowlevel we used taxadiene as a measure to quantify the production of thismolecule and authentic mass spectral fragmentation characteristics fromprevious reports⁴².

qPCR Measurements for Transcriptional Analysis of Engineered Strains

Transcriptional gene expression levels of each gene were detected byqPCR on mRNA isolated from the appropriate strains. To preventdegradation, RNA was stabilized before cell lysis using RNAprotectbacterial reagent (Qiagen). Subsequently, total RNA was isolated usingRNeasy mini kit (Qiagen) combined with nuclease based removal of genomicDNA contaminants. cDNA was amplified using iScript cDNA synthesis kit(Biorad). qPCR was carried out on a Bio-Rad iCycler using the iQ SYBRGreen Supermix (Biorad). The level of expression of rrsA gene, which isnot subject to variable expression, was used for normalization of qPCRvalues.⁵⁶ Table 3 has primers used for qPCR. For each primer pair, astandard curve was constructed with mRNA of E. coli as the template.

Example 1 Taxadiene Accumulation Exhibits Strong Non-Linear Dependenceon the Relative Strengths of the Upstream MEP and Downstream SyntheticTaxadiene Pathways

FIG. 1 b depicts the various ways by which promoters and gene copynumbers were combined to modulate the relative flux (or strength)through the upstream and downstream pathways of taxadiene synthesis. Atotal of 16 strains were constructed in order to de-bottleneck the MEPpathway, as well as optimally balance it with the downstream taxadienepathway. FIG. 2 a,b summarize the results of taxadiene accumulation ineach of these strains, with FIG. 2 a accentuating the dependence oftaxadiene accumulation on the upstream pathway for constant values ofthe downstream pathway, and FIG. 2 b the dependence on the downstreampathway for constant upstream pathway strength (see also Table 1 for thecalculation of the upstream and downstream pathway expression from thereported promoter strengths and plasmid copy numbers³³⁻³⁶). Clearly,there are maxima exhibited with respect to both upstream and downstreampathway expression. For constant downstream pathway expression (FIG. 2a), as the upstream pathway expression increases from very low levels,taxadiene production is increased initially due to increased supply ofprecursors to the overall pathway. However, after an intermediate value,further upstream pathway increases cannot be accommodated by thecapacity of the downstream pathway. This pathway imbalance leads to theaccumulation of an intermediate (see below) that may be eitherinhibitory to cells or simply indicate flux diversion to a competingpathway, ultimately resulting in taxadiene accumulation reduction.

For constant upstream pathway expression (FIG. 2 b), a maximum issimilarly observed with respect to the level of downstream pathwayexpression. This is attributed to an initial limitation of taxadieneproduction by low expression levels of the downstream pathway, which isthus rate limiting with respect to taxadiene production. At high levelsof downstream pathway expression we are likely seeing the negativeeffect of high copy number on cell physiology, hence, a maximum existswith respect to downstream pathway expression. These results demonstratethat dramatic changes in taxadiene accumulation can be obtained fromchanges within a narrow window of expression levels for the upstream anddownstream pathways. For example, a strain containing an additional copyof the upstream pathway on its chromosome under Trc promoter control(Strain 8, FIG. 2 a) produced 2000 fold more taxadiene than oneoverexpressing only the synthetic downstream pathway (Strain 1, FIG. 2a). Furthermore, changing the order of the genes in the downstreamsynthetic operon from GT (GPPS-TS) to TG (TS-GPPS) resulted in 2-3-foldincrease (strains 1-4 compared to 5, 8, 11 and 14). The observed resultsshow that the key to taxadiene overproduction is ample downstreampathway capacity and careful balancing between the upstream precursorpathway with the downstream synthetic taxadiene pathway. Altogether, theengineered strains established that the MEP pathway flux can besubstantial, if a wide range of expression levels for the endogenousupstream and synthetic downstream pathway are searched simultaneously.

Example 2 Chromosomal Integration and Fine Tuning of the Upstream andDownstream Pathways Further Enhances Taxadiene Production

To provide ample downstream pathway strength while minimizing theplasmid-borne metabolic burden³⁷, two new sets of 4 strains each wereengineered (strains 25-28 and 29-32) in which the downstream pathway wasplaced under the control of a strong promoter (T7) while keeping arelatively low number of 5 and 10 copies, respectively. It can be seen(FIG. 2 c) that, while the taxadiene maximum is maintained at highdownstream strength (strains 21-24), a monotonic response is obtained atthe low downstream pathway strength (strains 17-20, FIG. 2 c). Thisobservation prompted the construction of two additional sets of 4strains each that maintained the same level of downstream pathwaystrength as before but expressed very low levels of the upstream pathway(strains 25-28 and 29-32, FIG. 2 d). Additionally, the operon of theupstream pathway of the latter strain set was chromosomally integrated.It can be seen that not only is the taxadiene maximum recovered, albeitat very low upstream pathway levels, but a much greater taxadienemaximum is attained (300 mg/L). We believe this significant increase canbe attributed to a decrease in cell's metabolic burden. This wasachieved by 1) eliminating plasmid dependence through integration of thepathway into the chromosome and 2) attaining a fine balance between theupstream and downstream pathway expression.

The 32 recombinant constructs allowed us to adequately probe the modularpathway expression space and amplify ˜15000 fold improvement intaxadiene production. This is by far the highest production ofterpenoids from E. coli MEP isoprenoid pathway reported (FIG. 3 a).Additionally, the observed fold improvements in terpenoid production aresignificantly higher than those of reported combinatorial metabolicengineering approaches that searched an extensive genetic spacecomprising up to a billion combinatorial variants of the isoprenoidpathway.³⁰ This suggests that pathway optimization depends far more onfine balancing of the expression of pathway modules than multi-sourcecombinatorial gene optimization. The multiple maxima exhibited in thephenotypic landscape of FIG. 1 underscores the importance of probing theexpression space at sufficient resolution to identify the region ofoptimum overall pathway performance. FIG. 7 depicts the foldimprovements in taxadiene production from the modular pathway expressionsearch.

Example 3 Metabolite Inversely Correlates with Taxadiene Production andIdentification of Metabolite

Metabolomic analysis of the previous engineered strains identified an,as yet, unknown, metabolite byproduct that correlated strongly withpathway expression levels and taxadiene production (FIG. 3 and FIG. 8).Although the chemical identity of the metabolite was unknown, wehypothesized that it is an isoprenoid side-product, resulting frompathway diversion and has been anti-correlated as a direct variable tothe taxadiene production (FIG. 3 and FIG. 8) from the engineeredstrains. A critical attribute of our optimal strains is the finebalancing that alleviates the accumulation of this metabolite, resultingin higher taxadiene production. This balancing can be modulated atdifferent levels from chromosome, or different copy number plasmids,using different promoters, with significantly different taxadieneaccumulation.

Subsequently the corresponding peak in the gas chromatography-massspectrometry (GC-MS) chromatogram was identified as indole by GC-MS, ¹Hand ¹³C nuclear magnetic resonance (NMR) spectroscopy studies (FIG. 16).We found that taxadiene synthesis by strain 26 is severely inhibited byexogenous indole at indole levels higher than ˜100 mg/L (FIG. 15 b).Further increasing the indole concentration also inhibited cell growth,with the level of inhibition being very strain dependent (FIG. 15 c).Although the biochemical mechanism of indole interaction with theisoprenoid pathway is presently unclear, the results in FIG. 15 suggesta possible synergistic effect between indole and terpenoid compounds ofthe isoprenoid pathway in inhibiting cell growth. Without knowing thespecific mechanism, it appears strain 26 has mitigated the indole'seffect, which we carried forward for further study.

Example 4 Cultivation of Engineered Strains

In order to explore the taxadiene producing potential under controlledconditions for the engineered strains, fed batch cultivations of thethree highest taxadiene accumulating strains (˜60 mg/L from strain 22;˜125 mg/L from strain 17; ˜300 mg/L from strain 26) were carried out in1 L-bioreactors (FIG. 17). The fed batch cultivation studies werecarried out as liquid-liquid two-phase fermentation using a 20% (v/v)dodecane overlay. The organic solvent was introduced to prevent airstripping of secreted taxadiene from the fermentation medium, asindicated by preliminary findings. In defined media with controlledglycerol feeding, taxadiene productivity increased to 174±5 mg/L (SD),210±7 mg/L (SD), and 1020±80 mg/L (SD), respectively for strains 22, 17and 26 (FIG. 17 a). Additionally, taxadiene production significantlyaffected the growth phenotype, acetate accumulation and glycerolconsumption (FIG. 17 b-17 d).

FIG. 17 c shows that acetate accumulates in all strains initially,however after ˜60 hrs acetate decreases in strains 17 and 26 while itcontinues to increase in strain 22. This phenomenon highlights thedifferences in central carbon metabolism between high MEP flux strains(26 and 17) and low MEP flux strain (22). Additionally, this observationis another illustration of the good physiology that characterizes awell-balanced, -functioning strain. Acetic acid, as product of overflowmetabolism, is initially produced by all strains due to the high initialglycerol concentrations used in these fermentations and correspondinghigh glycerol pathway flux. This flux is sufficient for supplying alsothe MEP pathway, as well as the other metabolic pathways in the cell.

At ˜48 hrs, the initial glycerol is depleted, and the cultivationswitches to a fed-batch mode, during which low but constant glycerollevels are maintained. This results in a low overall glycerol flux,which, for strains with high MEP flux (strains 26 and 17), is mostlydiverted to the MEP pathway while minimizing overflow metabolism. As aresult acetic acid production is reduced or even totally eliminated.Regarding the decline in acetic acid concentration, it is possible thatacetic acid assimilation may have happened to some extent, although thiswas not further investigated from a flux analysis standpoint. Someevaporation and dilution due to glycerol feed are further contributingto the observed acetic acid concentration decline. In contrast, forstrains with low MEP flux (strain 22), flux diversion to the MEP pathwayis not very significant, so that glycerol flux still supplies all thenecessary carbon and energy requirements. Overflow metabolism continuesto occur leading to acetate secretion.

Clearly the high productivity and more robust growth of strain 26allowed very high taxadiene accumulation. Further improvements should bepossible through optimizing conditions in the bioreactor, balancingnutrients in the growth medium, and optimizing carbon delivery.

Example 5 Upstream and Downstream Pathway Expression Levels and CellGrowth Reveal Underlying Complexity

For a more detailed understanding of the engineered balance in pathwayexpression, we quantified the transcriptional gene expression levels ofdxs (upstream pathway) and TS (downstream pathway) for the highesttaxadiene producing strains and neighboring strains from FIGS. 2 c and d(strains 17, 22 and 25-32) (FIG. 4 a,b). As we hypothesized, expressionof the upstream pathway increased monotonically with promoter strengthand copy number for the MEP vector from: native promoter, Trc, T5, T7,and 10 copy and 20 copy plasmids, as seen in the DXS expression (FIG. 4a). Thus we found that dxs expression level correlates well with theupstream pathway strength. Similar correlations were found for the othergenes of the upstream pathway, idi, ispD and ispF (FIG. 14 a, b). In thedownstream gene expression, a ˜2 fold improvement was quantified aftertransferring the pathway from 5 to 10 copy plasmid (25-28 series and29-32 series) (FIG. 4 b).

While promoter and copy number effects influenced the gene expressions,secondary effects on the expression of the other pathway were alsoprominent. FIG. 4 a shows that for the same dxs expression cassettes, byincreasing the copy number of the TS plasmid from 5 to 10, dxsexpression was increased. Interestingly, the 5 copy TS plasmid (strains25-28 series) contained substantially higher taxadiene yields (FIG. 2 d)and less growth (FIG. 4 c,d) than the 10 copy TS plasmid. Controlplasmids that did not contain the taxadiene heterologous pathway, grewtwo fold higher densities, implying growth inhibition in the strains25-28 series is directly related to the taxadiene metabolic pathway andthe accumulation of taxadiene and its direct intermediates (FIG. 4 c).However the strain 29-32 series only showed modest increases in growthyield when comparing the empty control plasmids to the taxadieneexpressing strains (FIG. 4 d). This interplay between growth, taxadieneproduction, and expression level can also be seen with the plasmid-basedupstream expression vectors (strain 17 and 22). Growth inhibition wasmuch larger in the 10 copy, high taxadiene producing strain (strain 17)compared to the 20 copy, lower taxadiene producing strain (strain 22)(FIG. 4 d). Therefore product toxicity and carbon diversion to theheterologous pathway are likely to impede growth, rather thanplasmid-maintenance.

Also unexpected was the profound effect of the upstream expressionvector on downstream expression. FIG. 4 b would have two straight lines,if there was no cross talk between the pathways. However, ˜3 foldchanges in TS expression are observed for different MEP expressionvectors. This is likely due to significant competition for resources(raw material and energy) that are withdrawn from the host metabolismfor overexpression of both the four upstream and two downstream genes.³⁸Compared to the control strain 25c, a 4 fold growth inhibition wasobserved with strain 25 indicated that high overexpression of synthetictaxadiene pathway induced toxicity altering the growth phenotypecompared to the overexpression of native pathway (FIG. 4 c). However, asupstream expression increased, downstream expression was reduced,inadvertently in our case, to desirable levels to balance the upstreamand downstream pathways, minimizing growth inhibition (strain 26).

At the extreme of protein overexpression, T7 promoter-driven MEP pathwayresulted in severe growth inhibition, due to the synthesis of fourproteins at high level (strains 28 and 32). Expression of the TS genesby T7 does not appear to have as drastic effect by itself. The highrates of protein synthesis from the T7 induced expression (FIG. 4 ab)could lead to the down regulation of the protein synthesis machineryincluding components of housekeeping genes from early growth phaseimpairs the cell growth and lower the increase in biomass.^(39,40) Wehypothesized that our observed complex growth phenotypes are cumulativeeffects of (1) toxicity induced by activation of isoprenoid/taxadienemetabolism, and (2) and the effects of high recombinant proteinexpression. Altogether our multivariate-modular pathway engineeringapproach generated unexpected diversity in terpenoid metabolism and itscorrelation to the pathway expression and cell physiology. Rationaldesign of microbes for secondary metabolite production will require anunderstanding of pathway expression that goes beyond alinear/independent understanding of promoter strengths and copy numbers.However, simple, multivariate approaches, as employed here, canintroduce the necessary diversity to both (1) find high producers, and(2) provide a landscape for the systematic investigation of higher ordereffects that are dominant, yet under appreciated, in metabolic pathwayengineering.

Example 6 Engineering Taxol P450-Based Oxidation Chemistry in E. Coli

A central feature in the biosynthesis of Taxol is oxygenation atmultiple positions of the taxane core structure, reactions that areconsidered to be mediated by cytochrome P450-dependent monooxygenases.⁴¹After completion of the committed cyclization step of the pathway, theparent olefin, taxa-4(5),11(12)-diene, is next hydroxylated at the C5position by a cytochrome P450 enzyme, representing the first of eightoxygenation steps (of the taxane core) on route to Taxol (FIG. 6).⁴²Thus, a key step towards engineering Taxol-producing microbes is thedevelopment of P450-based oxidation chemistry in vivo. The firstoxygenation step is catalyzed by a cytochrome P450, taxadiene5α-hydroxylase, an unusual monooxygenase catalyzing the hydroxylationreaction along with double bond migration in the diterpene precursortaxadiene (FIG. 5 a). We report the first successful extension of thesynthetic pathway from taxadiene to taxadien-5α-ol and present the firstexamples of in vivo production of any functionalized Taxol intermediatesin E. coli.

In general, functional expression of plant cytochrome P450 ischallenging⁴³ due to the inherent limitations of bacterial platforms,such as the absence of electron transfer machinery, cytochrome P450reductases, and translational incompatibility of the membrane signalmodules of P450 enzymes due to the lack of an endoplasmic reticulum.Recently, through transmembrane (TM) engineering and the generation ofchimera enzymes of P450 and CPR reductases, some plant P450's have beenexpressed in E. coli for the biosynthesis of functionalmolecules.^(22,44) Still, every plant cytochrome p450 is unique in itstransmembrane signal sequence and electron transfer characteristics fromits reductase counterpart.⁴⁵ Our initial studies were focused onoptimizing the expression of codon-optimized synthetic taxadiene5α-hydroxylase by N-terminal transmembrane engineering and generatingchimera enzymes through translational fusion with the CPR redox partnerfrom the Taxus species, Taxus cytochrome P450 reductase (TCPR) (FIG. 5b).^(42,44,46) One of the chimera enzymes generated, At24T5αOH-tTCPR,was highly efficient in carrying out the first oxidation step with morethan 98% taxadiene conversion to taxadien-5α-ol and the byproduct5(12)-Oxa-3(11)-cyclotaxane (OCT) (FIG. 9 a).

Compared to the other chimeric P450s, At24T5αOH-tTCPR yielded two-foldhigher (21 mg/L) production of taxadien-5α-ol. As well, the weakeractivity of At8T5αOH-tTCPR and At24T5αOH-tTCPR resulted in accumulationof a recently characterized byproduct, a complex structuralrearrangement of taxadiene into the cyclic ether5(12)-Oxa-3(11)-cyclotaxane (OCT) (FIG. 9).⁴⁷ The byproduct accumulatedat approximately equal amounts as the desired product taxadien-5α-ol.The OCT formation was mediated by an unprecedented Taxus cytochrome P450reaction sequence involving oxidation and subsequent cyclizations.⁴⁷Thus, it seems likely that by protein engineering of the taxadiene5α-hydroxylases, termination of the reaction before cyclization willprevent the accumulation of such undesirable byproduct and channelingthe flux to taxadien-5α-ol could be achieved.

The productivity of strain 26-At24T5αOH-tTCPR was significantly reducedrelatively to that of taxadiene production by the parent strain 26 (˜300mg/L) with a concomitant increase in the accumulation of the previouslydescribed uncharacterized metabolite. No taxadiene accumulation wasobserved. Apparently, the introduction of an additional medium copyplasmid (10 copy, p10T7) bearing the At24T5αOH-tTCPR construct disturbedthe carefully engineered balance in the upstream and downstream pathwayof strain 26. Small scale fermentations were carried out in bioreactorsto quantify the alcohol production by strain 26-At24T5αOH-tTCPR. Thetime course profile of taxadien-5α-ol accumulation (FIG. 5 d) indicatesalcohol production of up to 58±3 mg/L with an equal amount of the OCTbyproduct produced. The observed alcohol production was ˜2400 foldhigher than previous production in S. cerevisiae. ¹⁷ Further increasesof taxadien-5α-ol production are likely possible through pathwayoptimization and protein engineering.

The multivariate-modular approach of pathway optimization has yieldedvery high producing strains of a critical Taxol precursor. Furthermore,the recombinant constructs have been equally effective in redirectingflux towards the synthesis of other complex pharmaceutical compounds,such as mono- , sesqui- and di-terpene (geraniol, linalool, amorphadieneand levopimaradiene) products engineered from the same pathway(unpublished results). Thus, our pathway engineering opens new avenuesto bio-synthesize natural products, especially in the context ofmicrobially-derived terpenoids for use as chemicals and fuels fromrenewable resources. By focusing on the universal terpenoid precursorsIPP and DMAPP, it was possible to, first, define the critical pathwaymodules and then modulate expression such as to optimally balance thepathway modules for seamless precursor conversion and minimalintermediate accumulation. This approach seems to be more effective thancombinatorial searches of large genetic spaces and also does not dependon a high throughput screen.

The MEP-pathway is energetically balanced and thus overall moreefficient in converting either glucose or glycerol to isoprenoids. Yet,during the past 10 years, many attempts at engineering the MEP-pathwayin E. coli to increase the supply of the key precursors IPP and DMAPPfor carotenoid^(28,47), sesquiterpenoid²³ and diterpenoid⁶¹overproduction met with limited success. This inefficiency wasattributed to unknown regulatory effects associated specifically withthe expression of the MEP-pathway in E. coli ²³. Here we provideevidence that such limitations are correlated with the accumulation ofthe metabolite indole, owing to the non-optimal expression of thepathway, which inhibits the isoprenoid pathway activity. Taxadieneoverproduction (under conditions of indole formation suppression),establishes the MEP-pathway as a very efficient route for biosynthesisof pharmaceutical and chemical products of the isoprenoid family. Onesimply needs to carefully balance the modular pathways as suggested byour multivariate-modular pathway engineering approach.

For successful microbial production of Taxol, demonstration of thechemical decoration of the taxadiene core by P450 based oxidationchemistry is essential.⁴¹ Cytochrome P450 monooxygenases constituteabout one half of the 19 distinct enzymatic steps in the Taxolbiosynthetic pathway. Characteristically, these genes show unusual highsequence similarity with each other (>70%) but low similarity (<30%)with other plant P450s.¹⁴ Due to the apparent similarity among Taxolmonooxygenases, expressing the proper activity for carrying out thespecific P450 oxidation chemistry was a particular challenge. Through TMengineering and construction of an artificial chimera enzyme with redoxpartner (TCPR), the Taxol cytochrome P450, taxadiene 5α-hydroxylase, wasfunctionally expressed in E. coli and shown to efficiently converttaxadiene to the corresponding alcohol product in vivo. Previous invitro studies have described the mechanism of converting taxadiene totaxadien-5α-ol by native taxadiene 5α-hydroxylase enzyme, but have notdiscussed the same conversion in vivo.⁴² This oxygenation andrearrangement reaction involves hydrogen abstraction from C20 positionof the taxadiene to form an allylic radical intermediate, followed byregio- and stereo-specific oxygen insertion at C5 position to yield thealcohol derivative (FIG. 5 a). The observed modest abundance of theenzyme in Taxus cells, and the low k_(cal) values suggested that the5α-hydroxylation step of Taxol biosynthesis is slow relative to thedownstream oxygenations and acylations in the Taxol pathway.⁴¹ Thus,engineering this step is key to Taxol synthesis, especially in thecontext of functional engineering of Taxol P450's in prokaryotic hostsuch as E. coli. In addition, this step was limiting in previous effortsof constructing the pathway in yeast.¹⁷ The engineered construct in thisstudy demonstrated >98% conversion of taxadiene in vivo with productaccumulation to ˜60 mg/L, a 2400 fold improvement over previousheterologous expression in yeast. This study has therefore succeeded notonly in synthesizing significantly greater amounts of key Taxolintermediates but also provides the basis for the synthesis ofsubsequent metabolites in the pathway by similar P450 chemistry.

Prior studies on structure-activity relationship on Taxol have shownthat alterations made either by removal or addition of some of itsfunctional groups did not change materially the activity of theTaxol.^(1,48) Such studies, however, were limited due to the restrictedability to introduce changes by chemical synthesis. Availability of amicrobial path for Taxol synthesis will drastically expand the space ofchemical modifications that can be examined, thus increasing theprobability of identifying more potent drug candidates. This offersexciting new opportunities for drug development, especially whenconsidering that such drug candidates will also be associated with anefficient production route.

In the past few decades, Taxol has spawned more interest within thescientific communities and general public than any other natural productdrug candidate.¹⁰ A major supply crisis is predicted from the projectedincrease in the use of Taxol or Taxol analogs for cancer chemotherapy,requiring new production routes, such as engineering of Taxolbiosynthetic machinery in microbes.⁸ While a few endophytic fungi ofTaxus species have been isolated capable of producing Taxol naturally,these microbial systems have yet to demonstrate suitability forsustainable production of the drug.⁴⁹ The results reported hererepresent a disruptive step towards a microbially-derived Taxol or Taxolprecursor, by removing the bottlenecks in the committed precursorpathway. Furthermore, the assembly of a synthetic pathway offers newpossibilities to tailor Taxol analogs by selectively engineering thepathway, thereby altering the taxane structure. These developments raiseoptimism for a microbial route for the cost-effective production ofTaxol or suitable Taxol precursors.

TABLE 1 Table 1. Ranking of upstream and downstream pathway expressionin arbitrary units (a.u.). The MEP pathway and GGPP synthase/taxadienesynthase pathway expression levels were estimated using published valuesof promoter strengths and copy number. Promoter strengths werecalculated as trc = 1, T5 = 1.96, T7 = 4.97, based on Brosius et. al.and Brunner et. al.^(33,34) Gene copy number was assigned by publishedcopy numbers for origin of replication for the different plasmids used,and one copy was used for integrations.³⁵⁻³⁷ Total expression wascalculated as the product of promoter strength and gene copy number.Native expression of the MEP pathway was arbitrarily assigned a value ofone, and changing the operon order of GGPP synthase and taxadiene wasassumed to affect taxadiene synthase expression by 20%.³⁵ Theseestimates of total expression guided engineering efforts. E - E coli K12MG1655 with two deletions ΔrecAΔendA; EDE3 - K12 MG1655 ΔrecAΔendA witha T7 RNA polymerase (DE3) integrated; MEP - dxs-idi-ispDF operon; GT -GPPS-TS operon; TG - TS-GPPS operon; Ch1 - 1 copy in chromosome; Trc -trc promoter; T5 - T5 promoter; T7 - T7 promoter; p5 - ~5 copy plasmid(pSC101);, p10 - ~10 copy plasmid (p15A); and p20 - ~20 copy plasmid(pBR322). Upstream MEP Downstream GT or TG Construct ExpressionExpression Taxadiene Strain (in addition to Pro- Strength* Copies Pro-Strength (mg/L) # Pathway engineering native copy)^($) Copies moter(a.u.) Construct GT/TG moter (a.u)^(#) Mean SD 1 Ep20TrcGT N/A 0 0  1*pBR322 20 1.00 20 0.02 0.01 2 ECh1TrcMEPp20TrcGT Chr.^($) 1 1 2 pBR32220 1.00 20 16.00 1.59 3 Ep5TrcMEPp20TrcGT pSC101 5 1 6 pBR322 20 1.00 202.55 0.21 4 Ep10TrcMEPp20TrcGT p15A 10 1 11  pBR322 20 1.00 20 1.930.323 5 Ep20TrcTG N/A 0 0 1 pBR322 20 1.20 24 0.19 0.01 6 Ep20T5GT N/A 00 1 pBR322 20 1.96 39 4.36 0.533 7 Ep20T5GTTrcT N/A 0 0 1 pBR322 20 2.9659 1.74 0.265 8 ECh1TrcMEPp20TrcTG Chr. 1 1 2 pBR322 20 1.20 24 45.442.28 9 ECh1TrcMEPp20T5GT Chr. 1 1 2 pBR322 20 1.96 39 16.52 0.84 10ECh1TrcMEPp20T5GT-TrcT Chr. 1 1 2 pBR322 20 2.96  59^(#) 2.52 0.30 11Ep5TrcMEPp20TrcTG pSC101 5 1 6 pBR322 20 1.20 24 7.41 0.63 12Ep5TrcMEPp20T5GT pSC101 5 1 6 pBR322 20 1.96 39 21.23 5.86 13Ep5TrcMEPp20T5TG-TrcT pSC101 5 1 6 pBR322 20 2.96 59 1.40 0.10 14Ep10TrcMEPp20TrcTG p15A 10 1 11  pBR322 20 1.20 24 2.36 0.29 15Ep10TrcMEPp20T5GT p15A 10 1 11  pBR322 20 1.96 39 8.91 2.94 16Ep10TrcMEPp20T5GT-TrcT p15A 10 1 11  pBR322 20 2.96 59 3.40 0.39 17EDE3p10TrcMEPp5T7TG p15A 10 1 11  pSC101 5 5.96 31 125.00 8.37 18EDE3p20TrcMEPp5T7TG pBR322 20 1 21  pSC101 5 5.96 31 58.00 3.07 19EDE3p20T5MEPp5T7TG pBR322 20 1.96 40  pSC101 5 5.96 31 44.00 2.88 20EDE3p20T7MEPp5T7TG pBR322 20 4.97 100  pSC101 5 5.96 31 32.00 6.63 21EDE3p5TrcMEPp10T7TG pSC101 5 1 6 p15A 10 5.96 61 7.00 1.40 22EDE3p20TrcMEPp10T7TG pBR322 20 1 21  p15A 10 5.96 61 59.00 5.57 23EDE3p20T5MEPp10T7TG pBR322 20 1.96 40  p15A 10 5.96 61 58.00 5.68 24EDE3p20T7MEPp10T7TG pBR322 20 4.97 100  p15A 10 5.96 61 20.00 0.73 25EDE3p5T7TG N/A 0 0 1 pSC101 5 5.96 31 19.00 8.23 26 EDE3Ch1TrcMEPp5T7TGChr. 1 1 2 pSC101 5 5.96 31 297.00 10.21 27 EDE3Ch1T5MEPp5T7TG Chr 11.96 3 pSC101 5 5.96 31 163.00 10.84 28 EDE3Ch1T7MEPp5T7TG Chr 1 4.97 6pSC101 5 5.96 31 26.00 0.32 29 EDE3p10T7TG N/A 0 0 1 p15A 10 5.96 618.00 0.39 30 EDE3Ch1TrcMEPp10T7TG Chr 1 1 2 p15A 10 5.96 61 30.00 1.5931 EDE3Ch1T5MEPp10T7TG Chr 1 1.96 3 p15A 10 5.96 61 40.00 0.56 32EDE3Ch1T7MEPp10T7TG Chr 1 4.97 6 p15A 10 5.96 61 17.00 0.41 *A value of1 was given to account for the native copies of the MEP pathway. ^($)MEPconstruct is localized in the chromosome. ^(#)p20T5GT-TrcT - Anadditional copy of gene T under separate promoter control (Trc) togetheroperon GT (under T5 promoter) on the same plasmid. For the calculationstrength, we have added the value as equivalent two separate operons(TrcT + T5GT = (20 × 1.96 + 20 × 1 = 59)) since our studies shows thatexpression of T was limited compared to G.

TABLE 2 Detail of all the plasmids constructed for the study Origin ofAntibiotic No Plasmid replication marker 1 p20T7MEP pBR322 Amp 2p20TrcMEP pBR322 Amp 3 p20T5MEP pBR322 Amp 4 p20T7MEPKmFRP pBR322 Km 5p20T5MEPKmFRP pBR322 Km 6 p20TrcMEPKm-FRP pBR322 Km 7 p10TrcMEP p15A Cm8 p5TrcMEP SC101 Spect 9 p20TrcGT pBR322 Amp 10 p20TrcTG pBR322 Amp 11p20T5GT pBR322 Amp 12 p10T7TG p15A Cm 13 p5T7TG SC101 Spect 14p10At8T5αOH-tTCPR p15A Cm 15 p10At24T5αOH-tTCPR p15A Cm 16p10At42T5αOH-tTCPR p15A Cm

TABLE 3 Details of the primer used for the cloningof plasmids, chromosomal delivery of theMEP pathway and qPCR measurements. SEQ ID NO Primer Name Sequences 1dxsNdeI(s) CGGCATATGAGTTTTGATATTGCCA AATACCCG 2 dxsNheI(a)CGGCTAGCTTATGCCAGCCAGGCCT TGATTTTG 3 idiNheI (s)CGCGGCTAGCGAAGGAGATATACAT ATGCAAACGGAACACGTCATTTTAT TG 4 idiEcoRI(a)CGGAATTCGCTCACAACCCCGGCAA ATGTCGG 5 ispDFEcoRI(s)GCGAATTCGAAGGAGATATACATAT GGCAACCACTCATTTGGATGTTTG 6 ispDFXhoI(a)GCGCTCGAGTCATTTTGTTGCCTTA ATGAGTAGCGCC 7 dxsidiispDFNcoI(s)TAAACCATGGGTTTTGATATTGCCA AATACCCG 8 dxsidiispDFKpnI(a)CGGGGTACCTCATTTTGTTGCCTTA ATGAGTAGCGC 9 dxsidiispDFXhoI(a)CGGCTCGAGTCATTTTGTTGCCTTA ATGAGTAGCGC 10 T5AgeI(s)CGTAACCGGTGCCTCTGCTAACCAT GTTCATGCCTTC 11 T5NheI(a)CTCCTTCGCTAGCTTATGCCAGCC 52 GGPPSNcoI(s) CGTACCATGGTTGATTTCAATGAATATATGAAAAGTAAGGC 12 GGPPSEcoRI(a) CGTAGAATTCACTCACAACTGACGAAACGCAATGTAATC 13 TXSEcoRI(s) CGTAGAATTCAGAAGGAGATATACATATGGCTAGCTCTACGGGTACG 14 TXSsaII(a) GATGGTCGACTTAGACCTGGATTGGATCGATGTAAAC 15 TXSNcoI(s) CGTACCATGGCTAGCTCTACGGGTA CG 16 TXSEcoRI(a)CGTAGAATTCTTAGACCTGGATTGG ATCGATGTAAAC 17 GGPPSEcoRI(s)CGTAGAATTCAGAAGGAGATATACA TATGTTTGATTTCAATGAATATATG AAAAGTAAGGC 18GGPPSSaII(a) GATGGTCGACTCACAACTGACGAAA CGCAATGTAATC 19 TSXhoI(a)GATGCTCGAGTTAGACCTGGATTGG ATCGATGTAAAC 20 pTrcSal(s)GCCGTCGACCATCATCATCATCATC 21 pTrcXba(a) GCAGTCTAGAGCCAGAACCGTTATGATGTCGGCGC 22 pCLBspEI(s) CGTGTCCGGAGCATCTAACGCTTGA GTTAAGCCGC 23pCLXbaI(a) GCAGTCTAGAGGAAACCTGTCGTGC CAGCTGC 24 KmFRPXhoI(s)GACGCTCGAGGAGCAATAACTAGCA TAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCTTGTGTA GGCTGGAGCTGCTTCG 25 KmFRPScaI(a)GACGAGTACTGAACGTCGGAATTGA TCCGTCGAC 26 KmFRPSacI(s)GACGGAGCTCGAGCAATAACTAGCA TAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCTTGTGTA GGCTGGAGCTGCTTCG 27 IntT7T5(s)ATGACGATTTTTGATAATTATGAAG TGTGGTTTGTCATTGCATTAATTGC GTTGCGCTCACTG 28IntTrc(s) ATGACGATTTTTGATAATTATGAAG TGTGGTTTGTCATTGGCATCCGCTTACAGACAAGCTGTG 29 Int(a) TTAGCGACGAAACCCGTAATACACTTCGTTCCAGCGCAGCCGACGTCGGA ATTGATCCGTCGAC 30 CYP17At8AANdeI(s)CGTACATATGGCTCTGTTATTAGCA GTTTTTGTGGCGAAATTTAACGAAG TAACCCAGC 31CYP17At24AANdeI(s) CGTACATATGGCTCTGTTATTAGCA GTTTTTTTTAGCATCGCTTTGAGTGCAATTG 32 CYP17At42AANdeI(s) CGTACATATGGCTCTGTTATTAGCAGTTTTTTTTCGCTCGAAACGTCATA GTAGCCTG 33 CYPLinkBamHI(a)CGCGGGATCCGGTGCTGCCCGGACG AGGGAACAGTTTGATTGAAAACCC 34 CPRBamHI(s)CGCGGGATCCCGCCGTGGTGGAAGT GATACACAG 35 CPRSalI(a)CGCGGTCGACTTACCAAATATCCCG TAAGTAGCGTCCATC 36 DXS qPCR (s)A T T C A A A A G C T T C C G G T C C T 37 DXS qPCR (a)A T C T G G C G A C A T T C G T T T T C 38 TS qPCR (s)G A C G A A C T G T C A C C C G A T T T 39 TS qPCR (a)G C T T C G C G G G T A G T A G A C A G 40 rrsA qPCR (s)A G G C C T T C G G G T T G T A A A G T 41 rrsa qPCR (a)A T T C C G A T T A A C G C T T G C A C

TABLE 4 Protein and Codon optimized nucleotide sequences. GGPP synthase(SEQ ID NO: 42) MFDFNEYMKSKAVAVDAALDKAIPLEYPEKIHESMRYSLLAGGKRVRPALCIAACELVGGSQDLAMPTACAMEMIHTMSLIHDDLPCMDNDDFRRGKPTNHKVFGEDTAVLAGDALLSFAFEHIAVATSKTVPSDRTLRVISELGKTIGSQGLVGGQVVDITSEGDANVDLKTLEWIHIHKTAVLLECSVVSGGILGGATEDEIARIRRYARCVGLLFQVVDDILDVTKSSEELGKTAGKDLLTDKATYPKLMGLEKAKEFAAELATRAKEELSSFDQIKAAPLLGLA DYIAFRQN (SEQ ID NO:43)ATGTTTGATTTCAATGAATATATGAAAAGTAAGGCTGTTGCGGTAGACGCGGCTCTGGATAAAGCGATTCCGCTGGAATATCCCGAGAAGATTCACGAATCGATGCGCTACTCCCTGTTAGCAGGAGGGAAACGCGTTCGTCCGGCATTATGCATCGCGGCCTGTGAACTCGTCGGCGGTTCACAGGACTTAGCAATGCCAACTGCTTGCGCAATGGAAATGATTCACACAATGAGCCTGATTCATGATGATTTGCCTTGCATGGACAACGATGACTTTCGGCGCGGTAAACCTACTAATCATAAGGTTTTTGGCGAAGATACTGCAGTGCTGGCGGGCGATGCGCTGCTGTCGTTTGCCTTCGAACATATCGCCGTCGCGACCTCGAAAACCGTCCCGTCGGACCGTACGCTTCGCGTGATTTCCGAGCTGGGAAAGACCATCGGCTCTCAAGGACTCGTGGGTGGTCAGGTAGTTGATATCACGTCTGAGGGTGACGCGAACGTGGACCTGAAAACCCTGGAGTGGATCCATATTCACAAAACGGCCGTGCTGCTGGAATGTAGCGTGGTGTCAGGGGGGATCTTGGGGGGCGCCACGGAGGATGAAATCGCGCGTATTCGTCGTTATGCCCGCTGTGTTGGACTGTTATTTCAGGTGGTGGATGACATCCTGGATGTCACAAAATCCAGCGAAGAGCTTGGCAAGACCGCGGGCAAAGACCTTCTGACGGATAAGGCTACATACCCGAAATTGATGGGCTTGGAGAAAGCCAAGGAGTTCGCAGCTGAACTTGCCACGCGGGCGAAGGAAGAACTCTCTTCTTTCGATCAAATCAAAGCCGCGCCACTGCTGGGCCTCGCCGATTACATTGCGTTTCGTCAGAAC Taxadiene synthase (SEQ ID NO: 44)MSSSTGTSKVVSETSSTIVDDIPRLSANYHGDLWHHNVIQTLETPFRESSTYQERADELVVKIKDMFNALGDGDISPSAYDTAWVARLATISSDGSEKPRFPQALNWVFNNQLQDGSWGIESHFSLCDRLLNTTNSVIALSVWKTGHSQVQQGAEFIAENLRLLNEEDELSPDFQIIFPALLQKAKALGINLPYDLPFIKYLSTTREARLTDVSAAADNIPANMLNALEGLEEVIDWNKIMRFQSKDGSFLSSPASTACVLMNTGDEKCFTFLNNLLDKFGGCVPCMYSIDLLERLSLVDNIEHLGIGRHFKQEIKGALDYVYRHWSERGIGWGRDSLVPDLNTTALGLRTLRMHGYNVSSDVLNNFKDENGRFFSSAGQTHVELRSVVNLFRASDLAFPDERAMDDARKFAEPYLREALATKISTNTKLFKEIEYVVEYPWHMSIPRLEARSYIDSYDDNYVWQRKTLYRMPSLSNSKCLELAKLDFNIVQSLHQEELKLLTRWWKESGMADINFTRHRVAEVYFSSATFEPEYSATRIAFTKIGCLQVLFDDMADIFATLDELKSFTEGVKRWDTSLLHEIPECMQTCFKVWFKLMEEVNNDVVKVQGRDMLAHIRKPWELYFNCYVQEREWLEAGYIPTFEEYLKTYAISVGLGPCTLQPILLMGELVKDDVVEKVHYPSNMFELVSLSWRLTNDTKTYQAEKARGQQASGIACYMKDNPGATEEDAIKHICRVVDRALKEASFEYFKPSNDIPMGCKSFIFNLRLCVQIFYKFIDGYGIANEEIKDYIRKVYIDPIQV (SEQ ID NO: 45)ATGTCTAGCTCTACGGGTACGTCTAAAGTCGTGAGTGAAACCTCATCGACGATCGTGGACGATATTCCACGCTTGTCGGCGAACTATCATGGAGATCTGTGGCATCATAACGTCATTCAGACATTGGAAACCCCGTTTCGCGAAAGTAGCACCTACCAGGAACGGGCAGATGAATTAGTCGTGAAAATCAAAGATATGTTTAATGCATTAGGAGATGGAGACATCTCGCCCAGCGCATATGATACGGCGTGGGTGGCTCGGTTGGCCACGATTAGCTCCGATGGCAGTGAAAAGCCGCGTTTCCCGCAGGCGCTGAACTGGGTGTTTAATAATCAATTGCAGGATGGCAGCTGGGGCATTGAATCTCACTTTAGCCTCTGTGACCGGTTACTCAACACGACAAACTCCGTAATTGCGTTGTCAGTTTGGAAAACGGGCCATAGCCAGGTTCAACAGGGCGCGGAATTTATCGCTGAAAATCTGCGCCTGCTGAACGAGGAGGACGAACTGTCACCCGATTTTCAGATTATTTTTCCGGCTTTACTCCAGAAAGCCAAAGCCTTAGGCATCAACCTGCCATATGATCTGCCGTTCATCAAGTATCTGTCTACTACCCGCGAAGCCCGTCTCACTGACGTCTCTGCGGCGGCGGACAATATTCCAGCGAACATGCTGAACGCACTGGAAGGGCTGGAAGAGGTTATCGACTGGAATAAAATCATGCGCTTCCAAAGCAAGGACGGTAGCTTCTTAAGCAGCCCAGCATCTACTGCTTGTGTTCTGATGAATACCGGAGACGAAAAGTGCTTTACGTTTCTGAACAATCTGCTGGACAAATTTGGGGGTTGTGTTCCTTGTATGTATTCCATTGATCTGTTGGAACGTCTGTCGCTGGTCGATAACATTGAACACTTAGGTATCGGCCGCCACTTCAAACAAGAAATCAAGGGGGCGTTGGATTATGTATACCGTCATTGGAGCGAGCGTGGTATTGGTTGGGGGCGCGATAGCTTGGTACCTGATCTGAACACCACTGCTTTGGGACTGCGCACTCTTCGTATGCACGGATACAACGTTAGTTCCGATGTCCTCAATAATTTCAAGGACGAGAACGGCCGTTTTTTCAGCTCGGCCGGTCAGACGCATGTTGAACTGCGGTCCGTAGTCAATCTCTTTCGCGCTAGTGATCTGGCTTCCCCGACGAGCGCGCTATGGACGATGCACGGAAGTTTGCCGAGCCGTATCTCCGCGAAGCCCTGGCCACCAAAATTTCAACCAACACCAAGCTTTTCAAAGAAATTGAGTATGTAGTAGAGTATCCGTGGCATATGTCTATTCCGCGCCTGGAAGCCCGCTCGTATATCGATTCTTACGATGACAATTATGTGTGGCAACGCAAAACACTGTACCGTATGCCCAGCCTGTCAAATAGTAAGTGTCTGGAGCTGGCGAAACTGGATTTCAACATTGTGCAATCCCTGCACCAAGAAGAGCTGAAATTACTGACTCGCTGGTGGAAGGAATCCGGCATGGCAGACATCAATTTTACGCGTCACCGTGTTGCAGAGGTGTACTTCTCCTCGGCGACCTTTGAGCCGGAGTATTCGGCCACACGTATTGCATTTACCAAGATTGGCTGCCTTCAGGTGCTTTTTGACGATATGGCGGATATTTTTGCGACACTTGATGAGCTTAAATCATTTACCGAAGGCGTGAAGCGTTGGGATACCTCTCTGTTGCATGAAATCCCCGAATGTATGCAGACCTGCTTCAAAGTTTGGTTCAAACTGATGGAAGAAGTGAACAACGACGTCGTGAAAGTTCAGGGTCGTGATATGTTAGCACACATCCGCAAGCCGTGGGAACTCTATTTCAATTGCTATGTGCAGGAGCGTGAATGGTTAGAAGCGGGCTACATTCCTACTTCGAAGAGTACTTAAAAACCTATGCCATTTCCGTCGGTTTAGGCCCGTGCACTCTGCAGCCTATCTTGCTGATGGGTGAGCTGGTAAAGGATGATGTGGTGGAAAAAGTTCACTACCCGTCGAATATGTTTGAACTGGTAAGTCTGAGTTGGCGTCTGACAAACGACACCAAAACGTACCAGGCAGAAAAGGCACGTGGGCAACAGGCAAGCGGTATCGCGTGTTATATGAAGGATAATCCGGGCGCTACTGAGGAAGATGCCATTAAGCATATCTGCCGTGTTGTGGATCGCGCTCTTAAAGAAGCGTCATTCGAATATTTTAAACCTAGTAATGATATTCCGATGGGTTGTAAGTCATTCATTTTCAATCTTCGCCTGTGCGTGCAAATTTTTTACAAATTTATTGACGGCTACGGAATCGCCAACGAAGAAATCAAAGACTATATTCGTAAAGTTTACATCGATCCAATCCA GGTCCytochrome P450 Taxadiene 5a-hydroxylase (T5αOH) (SEQ ID NO: 46)MDALYKSTVAKFNEVTQLDCSTESFSIALSAIAGILLLLLLFRSKRHSSLKLPPGKLGIPFIGESFIFLRALRSNSLEQFFDERVKKFGLVFKTSLIGHPTVVLCGPAGNRLILSNEEKLVQMSWPAQFMKLMGENSVATRRGEDHIVMRSALAGFFGPGALQSYIGKMNTEIQSHINEKWKGKDEVNVLPLVRELVFNISAILFFNIYDKQEQDRLHKLLETILVGSFALPIDLPGFGFHRALQGRAKLNKIMLSLIKKRKEDLQSGSATATQDLLSVLLTFRDDKGTPLTNDEILDNFSSLLHASYDTTTSPMALIFKLLSSNPECYQKVVQEQLEILSNKEEGEEITWKDLKAMKYTWQVAQETLRMFPPVFGTFRKAITDIQYDGYTIPKGWKLLWTTYSTHPKDLYFNEPEKFMPSRFDQEGKHVAPYTFLPFGGGQRSCVGWEFSKMEILLFVHHFVKTFSSYTPVDPDEKISG DPLPPLPSKGFSIKLFPRP(SEQ ID NO: 47) ATGGATGCCCTCTATAAGTCTACCGTGGCGAAATTTAACGAAGTAACCCAGCTGGATTGCAGCACTGAGTCATTTAGCATCGCTTTGAGTGCAATTGCCGGGATCTTGCTGTTGCTCCTGCTGTTTCGCTCGAAACGTCATAGTAGCCTGAAATTACCTCCGGGCAAACTGGGCATTCCGTTTATCGGTGAGTCCTTTATTTTTTTGCGCGCGCTGCGCAGCAATTCTCTGGAACAGTTCTTTGATGAACGTGTGAAGAAGTTCGGCCTGGTATTTAAAACGTCCCTTATCGGTCACCCGACGGTTGTCCTGTGCGGGCCCGCAGGTAATCGCCTCATCCTGAGCAACGAAGAAAAGCTGGTACAGATGTCCTGGCCGGCGCAGTTTATGAAGCTGATGGGAGAGAACTCAGTTGCGACCCGCCGTGGTGAAGATCACATTGTTATGCGCTCCGCGTTGGCAGGCTTTTTCGGCCCGGGAGCTCTGCAATCCTATATCGGCAAGATGAACACGGAAATCCAAAGCCATATTAATGAAAAGTGGAAAGGGAAGGACGAGGTTAATGTCTTACCCCTGGTGCGGGAACTGGTTTTTAACATCAGCGCTATTCTGTTCTTTAACATTTACGATAAGCAGGAACAAGACCGTCTGCACAAGTTGTTAGAAACCATTCTGGTAGGCTCGTTTGCCTTACCAATTGATTTACCGGGTTTCGGGTTTCACCGCGCTTTACAAGGTCGTGCAAAACTCAATAAAATCATGTTGTCGCTTATTAAAAAACGTAAAGAGGACTTACAGTCGGGATCGGCCACCGCGACGCAGGACCTGTTGTCTGTGCTTCTGACTTTCCGTGATGATAAGGGCACCCCGTTAACCAATGACGAAATCCTGGACAACTTTAGCTCACTGCTTCACGCCTCTTACGACACCACGACTAGTCCAATGGCTCTGATTTTCAAATTACTGTCAAGTAACCCTGAATGCTATCAGAAAGTCGTGCAAGAGCAACTCGAGATTCTGAGCAATAAGGAAGAAGGTGAAGAAATTACCTGGAAAGATCTTAAGGCCATGAAATACACGTGGCAGGTTGCGCAGGAGACACTTCGCATGTTTCCACCGGTGTTCGGGACCTTCCGCAAAGCGATCACGGATATTCAGTATGACGGATACACAATCCCGAAAGGTTGGAAACTGTTGTGGACTACCTATAGCACTCATCCTAAGGACCTTTACTTCAACGAACCGGAGAAATTTATGCCTAGTCGTTTCGATCAGGAAGGCAAACATGTTGCGCCCTATACCTTCCTGCCCTTTGGAGGCGGTCAGCGGAGTTGTGTGGGTTGGGAGTTCTCTAAGATGGAGATTCTCCTCTTCGTGCATCATTTCGTGAAAACATTTTCGAGCTATACCCCGGTCGATCCCGATGAAAAAATTTCCGGCGATCCACTGCCGCCGTTACCGAGCAAAGGGTTTTCAATCAAACTGTTC CCTCGTCCGTaxus NADPH: cytochrome P450 reductase (TCPR) (SEQ ID NO: 48)MQANSNTVEGASQGKSLLDISRLDHIFALLLNGKGGDLGAMTGSALILTENSQNLMILTTALAVLVACVFFFVWRRGGSDTQKPAVRPTPLVKEEDEEEEDDSAKKKVTIFFGTQTGTAEGFAKALAEEAKARYEKAVFKVVDLDNYAADDEQYEEKLKKEKLAFFMLATYGDGEPTDNAARFYKWFLEGKEREPWLSDLTYGVFGLGNRQYEHFNKVAKAVDEVLIEQGAKRLVPVGLGDDDQCIEDDFTAWREQVWPELDQLLRDEDDEPTSATPYTAAIPEYRVEIYDSVVSVYEETHALKQNGQAVYDIHHPCRSNVAVRRELHTPLSDRSCIHLEFDISDTGLIYETGDHVGVHTENSIETVEEAAKLLGYQLDTIFSVHGDKEDGTPLGGSSLPPPFPGPCTLRTALARYADLLNPPRKAAFLALAAHASDPAEAERLKFLSSPAGKDEYSQWVTASQRSLLEIMAEFPSAKPPLGVFFAAIAPRLQPRYYSISSSPRFAPSRIHVTCALVYGPSPTGRIHKGVCSNWMKNSLPSEETHDCSWAPVFVRQSNFKLPADSTTPIVMVGPGTGFAPFRGFLQERAKLQEAGEKLGPAVLFFGCRNRQMDYIYEDELKGYVEKGILTNLIVAFSREGATKEYVQHKMLEKASDTWSLIAQGGYLYVCGDAKGMARDVHRTLHTIVQEQESVDSSKAEFLVKKLQMDGRYLRDIW (SEQ ID NO: 49)ATGCAGGCGAATTCTAATACGGTTGAAGGCGCGAGCCAAGGCAAGTCTCTTCTGGACATTAGTCGCCTCGACCATATCTTCGCCCTGCTGTTGAACGGGAAAGGCGGAGACCTTGGTGCGATGACCGGGTCGGCCTTAATTCTGACGGAAAATAGCCAGAACTTGATGATTCTGACCACTGCGCTGGCCGTTCTGGTCGCTTGCGTTTTTTTTTTCGTTTGGCGCCGTGGTGGAAGTGATACACAGAAGCCCGCCGTACGTCCCACACCTTCTTGTTAAAGAAGAGGACGAAGAAGAAGAAGATGATAGCGCCAAGAAAAAGGTCACAATATTTTTTGGCACCCAGACCGGCACCGCCGAAGGTTTCGCAAAGGCCTTAGCTGAGGAAGCAAAGGCACGTTATGAAAAGGCGGTATTTAAAGTCGTGGATTTGGATAACTATGCAGCGGATGACGAACAGTACGAAGAGAAGTTGAAAAAGGAAAAGCTAGCGTTCTTCATGCTCGCCACCTACGGTGACGGCGAACCGACTGATAATGCCGCTCGCTTTTATAAATGGTTTCTCGAGGGTAAAGAGCGCGAGCCATGGTTGTCAGATCTGACTTATGGCGTGTTTGGCTTAGGTAACCGTCAGTATGAACACTTTAACAAGGTCGCGAAAGCGGTGGACGAAGTGCTCATTGAACAAGGCGCCAAACGTCTGGTACCGGTAGGGCTTGGTGATGATGATCAGTGCATTGAGGACGACTTCACTGCCTGGAGAGAACAAGTGTGGCCTGAGCTGGATCAGCTCTTACGTGATGAAGATGACGAGCCGACGTCTGCGACCCCGTACACGGCGGCTATTCCAGAATACCGGGTGGAAATCTACGACTCAGTAGTGTCGGTCTATGAGGAAACCCATGCGCTGAAACAAAATGGACAAGCCGTATACGATATCCACCACCCGTGTCGCAGCAACGTGGCAGTACGTCGTGAGCTGCATACCCCGCTGTCGGATCGTAGTTGTATTCATCTGGAATTCGATATTAGTGATACTGGGTTAATCTATGAGACGGGCGACCACGTTGGAGTTCATACCGAGAATTCAATTGAAACCGTGGAAGAAGCAGCTAAACTGTTAGGTTACCAACTGGATACAATCTTCAGCGTGCATGGGGACAAGGAAGATGGAACACCATTGGGCGGGAGTAGCCTGCCACCGCCGTTTCCGGGGCCCTGCACGCTGCGGACGGCGCTGGCACGTTACGCGGACCTGCTGAACCCTCCGCGCAAAGCCGCCTTCCTGGCACTGGCCGCACACGCGTCAGATCCGGCTGAAGCTGAACGCCTTAAATTTCTCAGTTCTCCAGCCGGAAAAGACGAATACTCACAGTGGGTCACTGCGTCCCAACGCAGCCTCCTCGAGATTATGGCCGAATTCCCCAGCGCGAAACCGCCGCTGGGAGTGTTTTTCGCCGCAATAGCGCCGCGCTTGCAACCTAGGTATTATAGCATCTCCTCCTCCCCGCGTTTCGCGCCGTCTCGTATCCATGTAACGTGCGCGCTGGTCTATGGTCCTAGCCCTACGGGGCGTATTCATAAAGGTGTGTGCAGCAACTGGATGAAGAATTCTTTGCCCTCCGAAGAAACCCACGATTGCAGCTGGGCACCGGTCTTTGTGCGCCAGTCAAACTTTAAACTGCCCGCCGATTCGACGACGCCAATCGTGATGGTTGGACCTGGAACCGGCTTCGCTCCATTTCGCGGCTTCCTTCAGGAACGCGCAAAACTGCAGGAAGCGGGCGAAAAATTGGGCCCGGCAGTGCTGTTTTTTGGGTGCCGCAACCGCCAGATGGATTACATCTATGAAGATGAGCTTAAGGGTTACGTTGAAAAAGGTATTCTGACGAATCTGATCGTTGCATTTTCACGAGAAGGCGCCACCAAAGAGTATGTTCAGCACAAGATGTTAGAGAAAGCCTCCGACACGTGGTCTTTAATCGCCCAGGGTGGTTATCTGTATGTTTGCGGTGATGCGAAGGGTATGGCCAGAGACGTACATCGCACCCTGCATACAATCGTTCAGGAACAAGAATCCGTAGACTCGTCAAAAGCGGAGTTTTTAGTCAAAAAGCTGCAAATGGATGGACGCTACTTACGGGATATTTGGReferences

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Having thus described several aspects of at least one embodiment of thisinvention, it is to be appreciated various alterations, modifications,and improvements will readily occur to those skilled in the art. Suchalterations, modifications, and improvements are intended to be part ofthis disclosure, and are intended to be within the spirit and scope ofthe invention. Accordingly, the foregoing description and drawings areby way of example only. Those skilled in the art will recognize, or beable to ascertain using no more than routine experimentation, manyequivalents to the specific embodiments of the invention describedherein. Such equivalents are intended to be encompassed by the followingclaims.

All references disclosed herein are incorporated by reference in theirentirety for the specific purpose mentioned herein.

What is claimed is:
 1. A method for increasing terpenoid production in acell that produces one or more terpenoids, comprising providing anEscherichia coli (E. coli) that produces isopentyl pyrophosphate (IPP)and dimethylallyl pyrophospate (DMAPP) through an upstreammethylerythritol pathway (MEP) and converts the IPP and DMAPP to aterpenoid through a recombinantly expressed downstream terpenoidsynthesis pathway; and culturing the E. coli to produce the terpenoid,wherein the accumulation of indole in the culture is controlled to below100 mg/L to thereby increase terpenoid production.
 2. The method ofclaim 1, wherein accumulation of indole in the culture is controlled bybalancing the upstream MEP pathway with the downstream terpenoidsynthesis pathway.
 3. The method of claim 1, wherein the step ofculturing comprises removing the accumulated indole.
 4. The method ofclaim 1, wherein the one or more terpenoids is a monoterpenoid, asesquiterpenoid, a diterpenoid, a triterpenoid or a tetraterpenoid. 5.The method of claim 4, wherein the one or more terpenoids is taxadieneor a taxol precursor.
 6. The method of claim 1 further comprisingmeasuring the amount or concentration of indole in the culture.
 7. Themethod of claim 6, wherein the method comprises measuring the amount orconcentration of indole two or more times.
 8. The method of claim 6,wherein the measured amount or concentration of indole is used to guidea process of producing one or more terpenoids.
 9. The method of claim 6,wherein the measured amount or concentration of indole is used to guidestrain construction.
 10. The method of claim 1, wherein the methodamplifies metabolic flux through IPP and DMAPP, and at least oneintermediate selected from geranyl diphosphate (GPP), geranylgeranyldiphosphate (GGPP), farnesyl diphosphate (FPP), and farnesyl geranyldiphosphate (FGPP).
 11. The method of claim 1, wherein the E. colirecombinantly expresses a geranylgeranyl diphosphate synthase (GGPS).12. The method of claim 1, wherein the E. coli has an amplified copynumber of the dxs, idi, ispD and ispF genes of the MEP pathway.
 13. Themethod of claim 1, wherein the terpenoid is geraniol, citronellol,nootkatone, cineol, limonene, eleutherobin, sarcodictyin, apseudopterosin, a ginkgolide, a stevioside, Rebaudioside A, sclareol,labdenediol, levopimaradiene, sandracopimaradiene or isopemaradiene. 14.A method for producing a terpenoid, comprising culturing an Escherichiacoli (E. coli) that produces isopentyl pyrophosphate (IPP) anddimethylallyl pyrophospate (DMAPP) through an upstream methylerythritolpathway (MEP) and which converts the IPP and DMAPP to a terpenoidthrough a recombinantly expressed downstream terpenoid synthesispathway, wherein the E. coli produces the terpenoid without accumulatingindole in the culture media at greater than 100 mg/L; wherein the E.coli has an amplified copy number of one or more of dxs, idi, ispD, andispF, and wherein the terpenoid is selected from taxadiene or taxolprecursor, citronellol, geraniol, nootkatone, cineol, limonene,eleutherobin, sarcodictyin, a pseudopterosin, a ginkgolide, astevioside, Rebaudioside A, sclareol, labdenediol, levopimaradiene,sandracopimaradiene and isopemaradiene; and recovering the terpenoid.